Academic Commons Search Resultshttp://academiccommons.columbia.edu/catalog.rss?f%5Bsubject_facet%5D%5B%5D=Biomedical+engineering&q=&rows=500&sort=record_creation_date+desc
Academic Commons Search Resultsen-usOptimization of Culture Conditions for Cartilage Tissue Engineering Using Synovium-Derived Stem Cellshttp://academiccommons.columbia.edu/catalog/ac:178862
Sampat, Sonal Ravinhttp://dx.doi.org/10.7916/D8NC5ZSHMon, 13 Oct 2014 00:00:00 +0000Osteoarthritis (OA) is the most common joint disease and the leading cause of disability among Americans. OA afflicts 20 million Americans and costs $128 billion in direct medical and work-related losses each year. Nearly 1/3 of OA patients in the United States are over 65 years of age and given the aging population of the "baby boomer" generation, the prevalence of this disease is predicted to increase dramatically in the coming decades. The disease is characterized by the degeneration of cartilage and progressive loss of normal structure and function. However, the harsh loading environment and the avascular nature of mature cartilage lead to a poor intrinsic healing capacity after injury. As a result, cell-based therapies, including tissue engineering strategies for growing clinically relevant grafts, are being intensively researched. An autologous cell source would be ideal for growing clinically relevant engineered cartilage; however, using cells from an osteoarthritic or injured tissue to grow engineered cartilage with mechanical and biochemical properties similar to healthy native tissue poses several challenges, including lack of healthy donor tissues and donor site morbidity. As a result, the clinical potential of mesenchymal stem cells (MSCs) has driven forward efforts toward their optimization for tissue engineering applications. Of these MSCs, synovium-derived stem cells (SDSCs) are being intensively researched due to their proximity to the defect site and high chondrogenic potential. To address the need for cell-based therapies, functional tissue engineering aims to restore cartilage function by culturing grafts in vitro that recapitulate the mechanical, biochemical, and structural framework of the tissue in order to have an increased chance of integration and survival upon in vivo implantation. While previous work in the lab has explored the utility of physiologically relevant stimuli for creating tissue grafts with chondrocytes, it has not yet been investigated for SDSCs. Therefore, in order to determine the potential of SDSCs as a tissue engineering strategy for growing clinically relevant cartilage grafts, this dissertation had four primary aims: (1) to initially produce tissue growth utilizing synovium-derived stem cells, (2) to utilize additional chemical, physical, and physico-chemical factors to further optimize growth of tissue engineered cartilage using SDSCs, (3) to characterize the response of SDSCs to the factors applied, and (4) to utilize the optimized culture techniques to translate the findings to clinically-relevant human cells. Our initial studies investigated the potential of using physiologically relevant growth factors during both 2D expansion and 3D culture conditions, from which a baseline culture protocol was established. We then sought to explore additional strategies to further optimize tissue growth. Motivated by the discrepancy in osmolarities between native and in vitro culture conditions, we first assessed the influence of adjusting the osmolarity of the baseline culture media. We found that culturing constructs under a more physiologic osmolarity (400 mOsM) was beneficial for tissue growth. Based on these findings implicating osmolarity as a key influencer of growth potential, we sought to determine and potentially manipulate some of the pathways involved in the osmotic response in an effort to further optimize and characterize our tissue-engineered cartilage constructs. Our results supported the role of the TRPV4 ion channel in our SDSC-seeded constructs as a key mechano-osmosensing mechanism. Through the culturing techniques evaluated, we were able to achieve native mechanical and biochemical measures of juvenile bovine cartilage using SDSCs. As has been shown in the literature, observed results in other species (bovine or canine) may not always correlate to findings using human cell sources, thereby prompting the emphasis for more relevant pre-clinical models. Therefore, our final studies sought to translate our treatment strategies to clinically relevant human cells from normal (non-diseased) and diseased (OA) SDSCs and chondrocytes in order to determine their utility. We were able to create a complete set of micropellet data for both SDSCs and chondrocytes to allow for comparisons. Overall, our micropellet results indicate that tissue condition (non-diseased vs OA) is the primary determinant of matrix synthesis. The research described in this dissertation has demonstrated the utility of SDSCs for strategies aimed at cartilage regeneration. We present the first studies to grow SDSC-seeded constructs to native properties of juvenile bovine chondrocytes. Therefore, utilization of the culture techniques presented here and other optimization strategies may hold key insights to developing a tissue using autologous/allogeneic SDSCs that can fully recreate native cartilage. In addition, the findings support the clinical potential of human SDSCs as a cell source for cartilage repair strategies.Biomedical engineeringBiomedical EngineeringDissertationsThe Effects of Arrhythmogenic Right Ventricular Cardiomyopathy-Causing Proteins on the Mechanical and Signaling Properties of Cardiac Myocyteshttp://academiccommons.columbia.edu/catalog/ac:178173
Hariharan, Venkateshhttp://dx.doi.org/10.7916/D84M933GTue, 30 Sep 2014 00:00:00 +0000Arrhythmogenic right ventricular cardiomyopathy (ARVC) is characterized by a high incidence of lethal ventricular arrhythmias, fibrofatty replacement of myocardium, and can account for up to 20% of sudden cardiac death (SCD) cases in the young. Typically involving autosomal dominant transmission, germline mutations in genes encoding desmosomal proteins have been identified as a cause of ARVC, although the pathogenesis of the disease is still unclear. While early detection and treatment can provide a normal life expectancy for the majority of patients, with less than 10% progressing to overt right ventricular failure, low genetic penetrance and epigenetic modifiers (such as endurance exercise) can make the condition difficult to diagnose. Addressing this clinical challenge requires a better understanding of the defective molecular mechanisms that underlie the disease. To that end, the goal of this dissertation is to provide insight into the effects of ARVC-causing mutant proteins on the mechanical and signaling properties of cardiac myocytes. Using elastography and histological techniques, we begin by characterizing the structural and mechanical properties of the native right ventricular myocardium, particularly the right ventricular apex (RVA). Because the RVA is a key site for development of arrhythmias and a potential pacing target, a careful characterization of its structure and mechanical properties are essential for understanding its role in cardiac physiology. In the first section of this dissertation, we perform a systematic analysis of the structural features and mechanical strains in the heart, focusing on the RVA region. More than half of ARVC patients exhibit one or more mutations in genes encoding desmosomal proteins. This has led many investigators to suggest that ARVC is a "disease of the desmosome" in which defective cell-cell adhesion plays a critical pathogenic role, although direct evidence for this hypothesis is lacking. To gain greater insights into potential mechanisms by which desmosomal mutations cause ARVC, we next characterize biomechanical properties and responses to shear stress (motivated by our results in the previous section) in neonatal rat ventricular myocytes expressing two distinct mutant forms of the desmosomal protein plakoglobin which have been linked to ARVC in patients. We show that ARVC-causing mutations in plakoglobin lead to altered cellular distribution of plakoglobin, without alterations in cell mechanical properties or certain early signaling pathways. The identification of defective molecular mechanisms that are common across ARVC-patients remains a strategic area of research. Specifically, recent studies have investigated the mechanistic basis for different ARVC-causing mutations in hopes of identifying common defects in a signaling pathway - information that could be used to develop diagnostic tests or identify therapeutic targets. In the last section of this dissertation, we investigate the effects of mutant plakophilin-2 expression, and repeat key experiments performed in the previous section to identify common defects in mechanical and signaling properties. We identify a common, underlying defect in ARVC pathogenesis. Specifically, we show that disease-causing mutations across different desmosomal proteins can cause the cell to respond abnormally to mechanical shear stress with respect to plakoglobin trafficking.Biomedical engineering, Biomechanicsvh2198Biomedical EngineeringDissertationsHybrid Segmentation of Anatomical Datahttp://academiccommons.columbia.edu/catalog/ac:177696
Imielinska, Celina Z.; Metaxes, Dimitris; Udupa, Jayaram; Jin, Yinpeng; Chen, Tinghttp://dx.doi.org/10.7916/D8125R75Mon, 29 Sep 2014 00:00:00 +0000We propose new hybrid methods for automated segmentation of radiological patient data and the Visible Human data. In this paper, we integrate boundary-based and region-based segmentation methods which amplifies the strength but reduces the weakness of both approaches. The novelty comes from combining a boundary-based method, the deformable model-based segmentation with region-based segmentation methods, the fuzzy connectedness and Voronoi Diagram-based segmentation, to develop hybrid methods that yield high precision, accuracy and efficiency. This work is a part of a NLM funded effort to provide a fully implemented and tested Visible Human Project Segmentation and Registration Toolkit (Insight).Bioinformatics, Biomedical engineering, Medical imaging and radiologyci42Biomedical Informatics, Biomedical EngineeringConferencesPhysically-based Deformation of High-Resolution 3D Lung Models for Augmented Reality based Medical Visualizationhttp://academiccommons.columbia.edu/catalog/ac:177618
Santhanam, Anand P.; Fidopiastis, Cali M.; Hamza-Lup, Felix G.; Rolland, Jannick P.; Imielinska, Celina Z.http://dx.doi.org/10.7916/D8TM78N5Wed, 24 Sep 2014 00:00:00 +0000Visualization tools using Augmented Reality Environments are effective in applications related to medical training, prognosis and expert interaction. Such medical visualization tools can also provide key visual insights on the physiology of deformable anatomical organs (e.g. lungs). In this paper we propose a deformation method that facilitates physically-based elastostatic deformations of 3D high-resolution polygonal models. The implementation of the deformation method as a pre-computation approach is shown for a 3D high-resolution lung model. The deformation is represented as an integration of the applied force and the local elastic property assigned to the 3D lung model. The proposed deformation method shows faster convergence to equilibrium as compared to other physically-based simulation methods. The proposed method also accounts for the anisotropic tissue elastic properties. The transfer functions are formulated in such a way that they overcome stiffness effects during deformations.Bioinformatics, Biomedical engineering, Medical imaging and radiologyci42Biomedical InformaticsConferencesDilation Based Modeling of Perfusion Datasetshttp://academiccommons.columbia.edu/catalog/ac:177624
Rosiene, J.; Imielinska, Celina Z.; Liu, Xin; Keating, S.http://dx.doi.org/10.7916/D8K35S7WWed, 24 Sep 2014 00:00:00 +0000A new approach to the modeling of the marker in Perfusion CT and Perfusion MR datasets is outlined and initial results given. The technique is based on estimation of the dilation and delay of an estimated bolus shape and a template fit to an new solution of the heat equation. Initial results are provided.Medical imaging and radiology, Bioinformatics, Biomedical engineeringci42Biomedical InformaticsConferencesChapter 1 : Hybrid Segmentation Methodshttp://academiccommons.columbia.edu/catalog/ac:177615
Imielinska, Celina Z.; Jin, Yinpeng; Angelini, Elsa D.; Metaxas, Dimitris; Udupa, Jayaram K.; Chen, Ting; Zhuge, Yinghttp://dx.doi.org/10.7916/D8BP01BXWed, 24 Sep 2014 00:00:00 +0000We propose a Hybrid Segmentation Engine that consists of component modules, for automated segmentation of radiological patient and the Visible Human data. We integrate boundary-based and region-based segmentation methods to exploit the strength of each method hopefully to cover the weakness of the other method.Bioinformatics, Biomedical engineering, Medical imaging and radiologyci42, ea179Biomedical Informatics, Biomedical EngineeringBook chaptersA Novel Drill Set for the Enhancement and Assessment of Robotic Surgical Performancehttp://academiccommons.columbia.edu/catalog/ac:177630
Ro, Charles Y.; Toumpoulis, Ioannis K.; Ashton, Jr., Robert C.; Imielinska, Celina Z.; Jebara, Tony ; Shin, Seung H.; Zipkin, J. D.; McGinty, James J.; Todd, George J.; DeRose, Jr., Joseph J.http://dx.doi.org/10.7916/D8J67FGCWed, 24 Sep 2014 00:00:00 +0000Background: There currently exist several training modules to improve performance during video-assisted surgery. The unique characteristics of robotic surgery make these platforms an inadequate environment for the development and assessment of robotic surgical performance. Methods: Expert surgeons (n=4) (greater than 50 clinical robotic procedures and greater than 2 years of clinical robotic experience) were compared to novice surgeons (n=17) (less than 5 clinical cases and limited laboratory experience) using the da Vinci Surgical System. Seven drills were designed to simulate clinical robotic surgical tasks. Performance score wascalculated by the equation Time to Completion + (minor error) x 5 + (major error) x 10. The Robotic Learning Curve (RLC) was expressed as a trend line of the performance scores corresponding to each repeated drill. Results: Performance scores for experts were better than novices in all 7 drills (p less than 0.05). The RLC for novices reflected an improvement in scores (p less than 0.05). In contrast, experts demonstrated a flat RLC for 6 drills and an improvement in one drill (p=0.027). Conclusion: This new drill set provides a framework for performance assessment during robotic surgery. The inclusion of particular drills and their role in training robotic surgeons of the future awaits larger validation studies.Medical imaging and radiology, Biomedical engineering, Surgeryci42, tj2008Biomedical Informatics, Computer ScienceConferencesPhysiologically-based Modeling and Visualization of Deformable Lungshttp://academiccommons.columbia.edu/catalog/ac:177606
Santhanam, Anand P.; Pattanaik, Sumant N.; Rolland, Jannick P.; Imielinska, Celina Z.; Norfleet, Jackhttp://dx.doi.org/10.7916/D8VM49T0Wed, 24 Sep 2014 00:00:00 +0000A real-time physiologically-based breathing model of lungs under normal and pathological scenario has been conceived and implemented. The algorithm developed for lung deformations under various breathing scenarios uses polygonal models of lungs. The method developed avoids the “stiffness” problem observed in Mass-Spring models. Hardware acceleration of the exhalation and the inhalation process is done using vertex shaders. The method of deformation is general and can be applied to any lung model.Biomedical engineering, Medical imaging and radiology, Bioinformaticsci42Biomedical InformaticsConferencesAdipose Tissue Quantification by Imaging Methods: A Proposed Classificationhttp://academiccommons.columbia.edu/catalog/ac:177581
Shen, Wei; Wang, ZiMian; Punyanita, Mark; Lei, Jianbo; Sinav, Ahmet; Kral, John G.; Imielinska, Celina Z.; Ross, Robert; Heymsfield, Steven B.http://dx.doi.org/10.7916/D8XS5SXVMon, 22 Sep 2014 00:00:00 +0000Recent advances in imaging techniques and understanding of differences in the molecular biology of adipose tissue has rendered classical anatomy obsolete, requiring a new classification of the topography of adipose tissue. Adipose tissue is one of the largest body compartments, yet a classification that defines specific adipose tissue depots based on their anatomic location and related functions is lacking. The absence of an accepted taxonomy poses problems for investigators studying adipose tissue topography and its functional correlates. The aim of this review was to critically examine the literature on imaging of whole body and regional adipose tissue and to create the first systematic classification of adipose tissue topography. Adipose tissue terminology was examined in over 100 original publications. Our analysis revealed inconsistencies in the use of specific definitions, especially for the compartment termed “visceral” adipose tissue. This analysis leads us to propose an updated classification of total body and regional adipose tissue, providing a well-defined basis for correlating imaging studies of specific adipose tissue depots with molecular processes.Medical imaging and radiology, Biomedical engineering, Molecular biologyws2003, as1018, ci42, sbh2Biomedical Informatics, Surgery, Institute of Human Nutrition, Pathology and Cell BiologyReviewsA Methodology for Evaluating Image Segmentation Algorithmshttp://academiccommons.columbia.edu/catalog/ac:177578
Udupa, Jayaram K.; LaBlanc, Vicki R.; Schmidt, Hilary; Imielinska, Celina Z.; Saha, Punam K.; Grevera, George J.; Zhuge, Ying; Molholt, Pat; Jin, Yinpeng; Currie, Leanne M.http://dx.doi.org/10.7916/D8FQ9V3DMon, 22 Sep 2014 00:00:00 +0000The purpose of this paper is to describe a framework for evaluating image segmentation algorithms. Image segmentation consists of object recognition and delineation. For evaluating segmentation methods, three factors - precision (reproducibility), accuracy (agreement with truth), and efficiency (time taken) – need to be considered for both recognition and delineation. To assess precision, we need to choose a figure of merit (FOM), repeat segmentation considering all sources of variation, and determine variations in FOM via statistical analysis. It is impossible usually to establish true segmentation. Hence, to assess accuracy, we need to choose a surrogate of true segmentation and proceed as for precision. To assess efficiency, both the computational and the user time required for algorithm and operator training and for algorithm execution should be measured and analyzed. Precision, accuracy, and efficiency are interdependent. It is difficult to improve one factor without affecting others. Segmentation methods must be compared based on all three factors. The weight given to each factor depends on application.Biomedical engineering, Computer science, Information technologyci42Biomedical Informatics, Center for Education Research and Evaluation, Biomedical EngineeringConferencesThe Effect of Varying Concentrations and Application Periods of Chondroitinase ABC on Tissue-Engineered Cartilagehttp://academiccommons.columbia.edu/catalog/ac:177400
Tong, Eric L; Kelly, Terri-Ann; O'Connell, G. D.; Hung, Clark T.http://dx.doi.org/10.7916/D8C827S5Fri, 19 Sep 2014 00:00:00 +0000Osteoarthritis, a chronic malady characterized by joint pain and swelling, is caused by damage to articular cartilage and is perpetuated by low-grade inflammation. Treatments for osteoarthritis do exist, but many treatments focus on coping with the disease rather than curing it. Surgical options that replace damaged cartilage tissue with that of donor cartilage tissue or cartilage tissue from other parts of articular joints face complications especially when the tissue is not of the correct size or does not have native-like properties. A more suitable treatment option for osteoarthritis is to develop an in vitro tissue-engineered cartilage construct that can be grown using the patient’s own cells and to surgically remove the patient’s damaged cartilage and replace it with the tissue-engineered cartilage. A challenge in developing such a treatment option is producing tissue-engineered cartilage with mechanical properties akin to those of native human articular cartilage. This challenge may be overcome by maximizing the production of type II collagen by the chondrocytes in vitro. One way to maximize collagen production is through the application of chondroitinase ABC, an enzyme which temporarily suppresses proteoglycans in the cartilage matrix to create more space for type II collagen to develop. In this study, two levels of cABC treatment were applied (“high” and “low”) to cartilage tissue constructs. The “low” cABC treated group received daily feeding of 0.075 U/mL from day 14 to 21 followed by a replacement of a chondrogenic media without cABC. The “high” cABC treated group received a single addition of 0.15 U/mL from day 14 to 16 followed by a replacement of chondrogenic media without cABC. At the end of 42 days, the constructs were subjected to mechanical testing and biochemical analyses. These analyses showed that the high cABC treatment yielded more native-like mechanical properties when compared to the low cABC treatment and the control results. Biochemical and histological analyses confirmed that the proteoglycan and collagen II content were higher in the low and high cABC treated groups when compared to the control. All analyses show that the most efficient application of chondroitinase ABC is through two day duration treatment of a higher concentration (0.15 U/mL).Biomedical engineeringelt2128, tnk6, cth6Columbia College, Biomedical EngineeringArticlesDistributed Augmented Reality with 3D Lung Dynamics - A Planning Tool Concepthttp://academiccommons.columbia.edu/catalog/ac:177136
Hamza-Lup, Felix G.; Santhanam, Anand P.; Imielinska, Celina Z.; Meeks, Sanford; Rolland, Jannick P.http://dx.doi.org/10.7916/D8445K0KThu, 11 Sep 2014 00:00:00 +0000Augmented Reality (AR) systems add visual information to the world by using advanced display techniques. The advances in miniaturization and reduced costs make some of these systems feasible for applications in a wide set of fields. We present a potential component of the cyber infrastructure for the operating room of the future; a distributed AR based software-hardware system that allows real-time visualization of 3D lung dynamics superimposed directly on the patient’s body. Several emergency events (e.g. closed and tension pneumothorax) and surgical procedures related to the lung (e.g. lung transplantation, lung volume reduction surgery, surgical treatment of lung infections, lung cancer surgery) could benefit from the proposed prototype.Medical imaging and radiology, Bioinformatics, Biomedical engineeringci42Biomedical InformaticsConferencesGenerating Classes of 3D Virtual Mandibles for AR-Based Medical Simulationhttp://academiccommons.columbia.edu/catalog/ac:177142
Hippalgaonkar, Neha R.; Sider, Alexa D.; Hamza-Lup, Felix G.; Santhanam, Anand P.; Jaganathan, Bala; Imielinska, Celina Z.; Rolland, Jannick P.http://dx.doi.org/10.7916/D8VM49SJThu, 11 Sep 2014 00:00:00 +0000Simulation and modeling represent promising tools for several application domains from engineering to forensic science and medicine. Advances in 3D imaging technology convey paradigms such as Augmented and Mixed Reality (AR/MR) inside promising simulation tools for the training industry. Motivated by the requirement for superimposing anatomically correct 3D models on a Human Patient Simulator (HPS) and visualizing them in an AR environment, the purpose of this research effort is to derive method for scaling a source human mandible to a target human mandible. Results show that, given a distance between two same landmarks on two different mandibles, a relative scaling factor may be computed. Using this scaling factor, results show that a 3D virtual mandible model can be made morphometrically equivalent to a real target-specific mandible within a 1.30 millimeter average error bound. The virtual mandible may be further used as a reference target for registering other anatomical ! models, such as the lungs, on the HPS. Such registration will be made possible by physical constraints among the mandible and the spinal column in the horizontal normal rest position.Bioinformatics, Biomedical engineering, Medical imaging and radiologyci42Biomedical InformaticsTechnical reportsModeling Air-flow in the Tracheobronchial Tree using Computational Fluid Dynamicshttp://academiccommons.columbia.edu/catalog/ac:177139
Kaya, Ilhan; Santhanam, Anand P.; Imielinska, Celina Z.; Rolland, Jannickhttp://dx.doi.org/10.7916/D80C4T99Thu, 11 Sep 2014 00:00:00 +0000In this paper, we present a biomechanical framework to model air-flow inside the bronchus and deformations across the tracheobronchial tree, pipeline for the simulator, theory and initial steps to realize this framework on a highly parallel graphical processing unit (GPU). We discuss the main challenges expected and encountered to date. By using computational fluid dynamics (CFD) and computational solid dynamics (CSD) principles, we propose a numerical simulation framework that includes a biomechanical model of the tracheobronchial tree to simulate air flow inside the tree, on GPU in real-time. The proposed 3D biomechanical model to simulate the air inside the lungs coupled with a deformation model of the tracheobronchial tree, expressed through fluid-structure interaction, can be used to predict the transformations of the voxels from a 4D computed tomography (4DCT) dataset. Additionally, the proposed multi-functional CFD and CSD based framework is suitable for clinical applications such as adaptive lung radiotherapy, and a regional alveolar ventilation estimation.Biomedical engineering, Bioinformatics, Biomechanicsci42Biomedical InformaticsConferencesMerging Augmented Reality and Anatomically Correct 3D Models in the Development of a Training Tool for Endotracheal Intubationhttp://academiccommons.columbia.edu/catalog/ac:177145
Rolland, Jannick; Davis, Larry; Hamza-Lup, Felix G.; Norfleet, Jack; Imielinska, Celina Z.; Kerner, Karen F.http://dx.doi.org/10.7916/D8QV3K1SThu, 11 Sep 2014 00:00:00 +0000Augmented reality is often used for medical training systems in which the user visualizes 3D information superimposed on the real world. In this context, we introduce a augmented reality tool to train the medical practitioner hand-eye coordination in performing critical procedures such as endotracheal intbation.Biomedical engineering, Bioinformatics, Biomechanicsci42, kfk9Biomedical Informatics, Computer Science, MedicineConferencesStatistical Bilateral Asymmetry Measurement in Brain Imageshttp://academiccommons.columbia.edu/catalog/ac:177036
Liu, Xin; Ogden, Robert T.; Imielinska, Celina Z.; Laine, Andrew F.; Connolly Jr., E. Sander; D'Ambrosio, Anthonyhttp://dx.doi.org/10.7916/D88W3BS2Tue, 09 Sep 2014 00:00:00 +0000We present an improvement of an automated generic methodology for symmetry identification, asymmetry quantification, and segmentation of brain pathologies, utilizing the inherent bi-fold mirror symmetry in brain imagery. In the pipeline of operations starting with detection of the symmetry axis, hemisphere-wise cross registration, statistical correlation and quantification of asymmetries, we segment a target brain pathology. The detection of pathological difference left to right in brain imagery is complicated by normal variations as well as geometric misalignment in anatomical structures between two hemispheres. Introducing hemisphere-wise registration and spatial correlation makes our approach perform robustly in the presence of normal asymmetries and systematic artifacts such as bias field and acquisition noise.Medical imaging and radiology, Biomedical engineering, Bioinformaticsxl2104, to166, ci42, al418, esc2181, ad3197Radiation Oncology, Neurological Surgery, Biomedical Informatics, Computer Science, Biostatistics, Biomedical EngineeringConferencesAutomatic Correction of the 3D Orientation of the Brain Imageryhttp://academiccommons.columbia.edu/catalog/ac:177039
Liu, Xin; Imielinska, Celina Z.; Connolly Jr., E. Sander; D'Ambrosio, Anthonyhttp://dx.doi.org/10.7916/D81C1VBBTue, 09 Sep 2014 00:00:00 +0000Classification of human brain pathologies can be guided by the estimation of the departure of 3D internal structures from the normal bilateral symmetry. However symmetry based analysis can 't be precisely carried out when the 3D brain orientation is misaligned, a common occurrence in clinical practice. In this paper, a technique to automatically identify the symmetry plane and correct the 3D orientation of volumetric brain images in a cost effective way is developed. The algorithm seeks the best sampling strategies to realign 3D volumetric representation of the brain within scanner coordinate system. The inertia matrix is computed on the sampled brain, and the principle axes are derived from the eigen vectors of the inertia matrix. The technique is demonstrated on MR and CT brain images and the detected symmetry plane that is orthogonal to the principle vectors is provided. A spatial affine transform is applied to rotate the 3D brain images and align them within the coordinate system of the scanner. The corrected brain volume is re-sliced such that each planar image represents the brain at the same axial level.Medical imaging and radiology, Biomedical engineering, Bioinformaticsxl2104, ci42, esc2181, ad3197Neurological Surgery, Radiation Oncology, Biomedical Informatics, Computer ScienceConferencesMulti-scale Modeling of Trauma Injuryhttp://academiccommons.columbia.edu/catalog/ac:177003
Imielinska, Celina Z.; Przekwas, Andrzej; Tan, X. G.http://dx.doi.org/10.7916/D8XK8D1QTue, 09 Sep 2014 00:00:00 +0000We develop a multi-scale high fidelity biomechanical and physiologically-based modeling tools for trauma (ballistic/impact and blast) injury to brain, lung and spinal cord for resuscitation, treatment planning and design of personnel protection. Several approaches have been used to study blast and ballistic/impact injuries. Dummy containing pressure sensors and synthetic phantoms of human organs have been used to study bomb blast and car crashes. Large animals like pigs also have been equipped with pressure sensors exposed to blast waves. But these methods do not anatomically and physiologically biofidelic to humans, do not provide full optimization of body protection design and require animal sacrifice. Anatomy and medical image based high-fidelity computational modeling can be used to analyze injury mechanisms and to optimize the design of body protection. This paper presents novel approach of coupled computational fluid dynamics (CFD) and computational structures dynamics (CSD) to simulate fluid (air, cerebrospinal fluid) solid (cranium, brain tissue) interaction during ballistic/blast impact. We propose a trauma injury simulation pipeline concept staring from anatomy and medical image based high fidelity 3D geometric modeling, extraction of tissue morphology, generation of computational grids, multiscale biomechanical and physiological simulations, and data visualization.Medical imaging and radiology, Biomedical engineering, Bioinformaticsci42Radiation Oncology, Biomedical Informatics, Computer ScienceArticlesQuantification of Diffusion-weighted Images (DWI) and Apparent Diffusion Coefficient Maps (ADC) in the Detection of Acute Strokehttp://academiccommons.columbia.edu/catalog/ac:177054
Tulipano, Paola K.; Millar, William S.; Imielinska, Celina Z.; Liu, Xin; Rosiene, Joel; D'Ambrosio, Anthony L.http://dx.doi.org/10.7916/D8DJ5D4XTue, 09 Sep 2014 00:00:00 +0000Magnetic resonance (MR) imaging is an imaging modality that is used in the management and diagnosis of acute stroke. Common MR imaging techniques such as diffusion weighted imaging (DWI) and apparent diffusion coefficient maps (ADC) are used routinely in the diagnosis of acute infarcts. However, advances in radiology information systems and imaging protocols have led to an overload of image information that can be difficult to manage and time consuming. Automated techniques to assist in the identification of acute ischemic stroke can prove beneficial to 1) the physician by providing a mechanism for early detection and 2) the patient by providing effective stroke therapy at an early stage. We have processed DW images and ADC maps using a novel automated Relative Difference Map (RDM) method that was tailored to the identification and delineation of the stroke region. Results indicate that the technique can delineate regions of acute infarctions on DW images and ADC maps. A formal evaluation of the RDM algorithm was performed by comparing accuracy measurementsbetween 1) expert generated ground truths with the RDM delineated DWI infarcts and 2) RDM delineated DWI infarcts with RDM delineated ADC infarcts. The accuracy measurements indicate that the RDM delineated DWI infarcts are comparable to the expert generated ground truths. The true positive volume fraction value (TPVF), between RDM delineated DWI and ADC infarcts, is nonzero for all cases with an acute infarct while the value for non-acute cases remains zero.Bioinformatics, Medical imaging and radiology, Biomedical engineeringpkt2, wsm8, ci42Radiation Oncology, Biomedical Informatics, Computer Science, RadiologyConferencesKeratinocyte cytoskeletal roles in cell sheet engineeringhttp://academiccommons.columbia.edu/catalog/ac:180214
Wei, Qi; Reidler, Daniel; Shen, Min Ye; Huang, Haydenhttp://dx.doi.org/10.7916/D8CJ8BTWMon, 08 Sep 2014 00:00:00 +0000Background: There is an increasing need to understand cell-cell interactions for cell and tissue engineering purposes, such as optimizing cell sheet constructs, as well as for examining adhesion defect diseases. For cell-sheet engineering, one major obstacle to sheet function is that cell sheets in suspension are fragile and, over time, will contract. While the role of the cytoskeleton in maintaining the structure and adhesion of cells cultured on a rigid substrate is well-characterized, a systematic examination of the role played by different components of the cytoskeleton in regulating cell sheet contraction and cohesion in the absence of a substrate has been lacking. Results: In this study, keratinocytes were cultured until confluent and cell sheets were generated using dispase to remove the influence of the substrate. The effects of disrupting actin, microtubules or intermediate filaments on cell-cell interactions were assessed by measuring cell sheet cohesion and contraction. Keratin intermediate filament disruption caused comparable effects on cell sheet cohesion and contraction, when compared to actin or microtubule disruption. Interfering with actomyosin contraction demonstrated that interfering with cell contraction can also diminish cell cohesion. Conclusions: All components of the cytoskeleton are involved in maintaining cell sheet cohesion and contraction, although not to the same extent. These findings demonstrate that substrate-free cell sheet biomechanical properties are dependent on the integrity of the cytoskeleton network.Biomedical engineeringBiomedical EngineeringArticlesIdentification of recurring patterns in fractionated atrial electrograms using new transform coefficientshttp://academiccommons.columbia.edu/catalog/ac:182684
Ciaccio, Edward J.; Biviano, Angelo; Whang, William; Garan, Hasanhttp://dx.doi.org/10.7916/D8SJ1HZTMon, 08 Sep 2014 00:00:00 +0000Identification of recurrent patterns in complex fractionated atrial electrograms (CFAE) has been used to differentiate paroxysmal from persistent atrial fibrillation (AF). Detection of the atrial CFAE patterns might therefore be assistive in guiding radiofrequency catheter ablation to drivers of the arrhythmia. In this study a technique for robust detection and classification of recurrent CFAE patterns is described. CFAE were obtained from the four pulmonary vein ostia, and from the anterior and posterior left atrium, in 10 patients with paroxysmal AF and 10 patients with longstanding persistent AF (216 recordings in total). Sequences 8.4 s in length were analyzed (8,192 sample points, 977 Hz sampling). Among the 216 sequences, two recurrent patterns A and B were substituted for 4 and 5 of the sequences, respectively. To this data, random interference, and random interference + noise were separately added. Basis vectors were constructed using a new transform that is derived from ensemble averaging. Patterns A and B were then detected and classified using a threshold level of Euclidean distance between spectral signatures as constructed with transform coefficients. In the presence of interference, sensitivity to detect and distinguish two patterns A and B was 96.2%, while specificity to exclude nonpatterns was 98.0%. In the presence of interference + noise, sensitivity was 89.1% while specificity was 97.0%. Transform coefficients computed from ensemble averages can be used to succinctly quantify synchronized patterns present in AF data. The technique is useful to automatically detect recurrent patterns in CFAE that are embedded in interference without user bias. This quantitation can be implemented in real-time to map the AF substrate prior to and during catheter ablation.Biomedical engineeringejc6, ab542, ww42, hg2017MedicineArticlesReview of Biomedical Image Processing. Edited by Thomas Martin Deserno. Springer-Verlag New York, LLC; 2011, 595 pageshttp://academiccommons.columbia.edu/catalog/ac:182824
Ciaccio, Edward J.http://dx.doi.org/10.7916/D80V8B4MMon, 08 Sep 2014 00:00:00 +0000This article is a review of the book: 'Biomedical Image Processing', by Thomas M. Deserno, which is published by Springer-Verlag. Salient information that will be useful to decide whether the book is relevant to topics of interest to the reader, and whether it might be suitable as a course textbook, are presented in the review. This includes information about the book details, a summary, the suitability of the text in course and research work, the framework of the book, its specific content, and conclusions.Biomedical engineeringejc6MedicineReviewsA new LMS algorithm for analysis of atrial fibrillation signalshttp://academiccommons.columbia.edu/catalog/ac:182618
Ciaccio, Edward J.; Biviano, Angelo B.; Whang, William; Garan, Hasanhttp://dx.doi.org/10.7916/D8NZ8603Mon, 08 Sep 2014 00:00:00 +0000A biomedical signal can be defined by its extrinsic features (x-axis and y-axis shift and scale) and intrinsic features (shape after normalization of extrinsic features). In this study, an LMS algorithm utilizing the method of differential steepest descent is developed, and is tested by normalization of extrinsic features in complex fractionated atrial electrograms (CFAE). Equations for normalization of x-axis and y-axis shift and scale are first derived. The algorithm is implemented for real-time analysis of CFAE acquired during atrial fibrillation (AF). Data was acquired at a 977 Hz sampling rate from 10 paroxysmal and 10 persistent AF patients undergoing clinical electrophysiologic study and catheter ablation therapy. Over 24 trials, normalization characteristics using the new algorithm with four weights were compared to the Widrow-Hoff LMS algorithm with four tapped delays. The time for convergence, and the mean squared error (MSE) after convergence, were compared. The new LMS algorithm was also applied to lead aVF of the electrocardiogram in one patient with longstanding persistent AF, to enhance the F wave and to monitor extrinsic changes in signal shape. The average waveform over a 25 s interval was used as a prototypical reference signal for matching with the aVF lead. Based on the derivation equations, the y-shift and y-scale adjustments of the new LMS algorithm were shown to be equivalent to the scalar form of the Widrow-Hoff LMS algorithm. For x-shift and x-scale adjustments, rather than implementing a long tapped delay as in Widrow-Hoff LMS, the new method uses only two weights. After convergence, the MSE for matching paroxysmal CFAE averaged 0.46 ± 0.49μV2/sample for the new LMS algorithm versus 0.72 ± 0.35μV2/sample for Widrow-Hoff LMS. The MSE for matching persistent CFAE averaged 0.55 ± 0.95μV2/sample for the new LMS algorithm versus 0.62 ± 0.55μV2/sample for Widrow-Hoff LMS. There were no significant differences in estimation error for paroxysmal versus persistent data. From all trials, the mean convergence time was approximately 1 second for both algorithms. The new LMS algorithm was useful to enhance the electrocardiogram F wave by subtraction of an adaptively weighted prototypical reference signal from the aVF lead. The extrinsic weighting over 25 s demonstrated that time-varying functions such as patient respiration could be identified and monitored. A new LMS algorithm was derived and used for normalization of the extrinsic features in CFAE and for electrocardiogram monitoring. The weighting at convergence provides an estimate of the degree of similarity between two signals in terms of x-axis and y-axis shift and scale. The algorithm is computationally efficient with low estimation error. Based on the results, proposed applications include monitoring of extrinsic and intrinsic features of repetitive patterns in CFAE, enhancement of the electrocardiogram F wave and monitoring of time-varying signal properties, and to quantitatively characterize mechanistic differences in paroxysmal versus persistent AF.Biomedical engineeringejc6, ab542, ww42, hg2017MedicineArticlesForce sensor in simulated skin and neural model mimic tactile SAI afferent spiking response to ramp and hold stimulihttp://academiccommons.columbia.edu/catalog/ac:181363
Kim, Elmer; Wellnitz, Scott; Bourdon, Sarah; Lumpkin, Ellen A.; Gerling, Gregoryhttp://dx.doi.org/10.7916/D8XW4H5BMon, 08 Sep 2014 00:00:00 +0000The next generation of prosthetic limbs will restore sensory feedback to the nervous system by mimicking how skin mechanoreceptors, innervated by afferents, produce trains of action potentials in response to compressive stimuli. Prior work has addressed building sensors within skin substitutes for robotics, modeling skin mechanics and neural dynamics of mechanotransduction, and predicting response timing of action potentials for vibration. The effort here is unique because it accounts for skin elasticity by measuring force within simulated skin, utilizes few free model parameters for parsimony, and separates parameter fitting and model validation. Additionally, the ramp-and-hold, sustained stimuli used in this work capture the essential features of the everyday task of contacting and holding an object. This systems integration effort computationally replicates the neural firing behavior for a slowly adapting type I (SAI) afferent in its temporally varying response to both intensity and rate of indentation force by combining a physical force sensor, housed in a skin-like substrate, with a mathematical model of neuronal spiking, the leaky integrate-and-fire. Comparison experiments were then conducted using ramp-and-hold stimuli on both the spiking-sensor model and mouse SAI afferents. The model parameters were iteratively fit against recorded SAI interspike intervals (ISI) before validating the model to assess its performance. Model-predicted spike firing compares favorably with that observed for single SAI afferents. As indentation magnitude increases (1.2, 1.3, to 1.4 mm), mean ISI decreases from 98.81 ± 24.73, 54.52 ± 6.94, to 41.11 ± 6.11 ms. Moreover, as rate of ramp-up increases, ISI during ramp-up decreases from 21.85 ± 5.33, 19.98 ± 3.10, to 15.42 ± 2.41 ms. Considering first spikes, the predicted latencies exhibited a decreasing trend as stimulus rate increased, as is observed in afferent recordings. Finally, the SAI afferent’s characteristic response of producing irregular ISIs is shown to be controllable via manipulating the output filtering from the sensor or adding stochastic noise. This integrated engineering approach extends prior works focused upon neural dynamics and vibration. Future efforts will perfect measures of performance, such as first spike latency and irregular ISIs, and link the generation of characteristic features within trains of action potentials with current pulse waveforms that stimulate single action potentials at the peripheral afferent.Biomedical engineeringeal2166DermatologyArticlesEngineering Lipid-stabilized Microbubbles for Magnetic Resonance Imaging guided Focused Ultrasound Surgeryhttp://academiccommons.columbia.edu/catalog/ac:175647
Feshitan, Jameel A.http://dx.doi.org/10.7916/D8BZ647VTue, 15 Jul 2014 00:00:00 +0000Lipid-stabilized microbubbles are gas-filled microspheres encapsulated with a phospholipid monolayer shell. Because of the high echogenicity provided by its highly compressible gas core, these microbubbles have been adapted as ultrasound contrast agents for a variety of applications such as contrast-enhanced ultrasonography (CEUS), targeted drug delivery and metabolic gas transport. Recently, these lipid-stabilized microbubbles have demonstrated increased potential as theranostic (therapy + diagnostics) agents for non-invasive surgery with focused ultrasound (FUS). For instance, their implementation has reduced the acoustic intensity threshold needed to open the blood-brain-barrier (BBB) with FUS, which potentially allows for the localized delivery of drugs to treat neurodegenerative diseases such as Alzheimer's, Parkinson's and Huntington's diseases. However, the effectiveness of microbubbles for this application is dependent on successful microbubble engineering. One necessary improvement is the development and utilization of monodisperse microbubbles of varying size classes. Another design improvement is the development of a microbubble construct whose fragmentation state during or after FUS surgery can be tracked by magnetic resonance imaging (MRI). Thus, in this thesis, we describe a method to generate and select lipid-coated gas-filled microbubbles of specific size fractions based on their migration in a centrifugal field. We also detail the design and characterization of size-selected lipid-coated microbubbles with shells containing the magnetic resonance (MR) contrast media Gadolinium (Gd(III)), for utility in both MR and ultrasound imaging. Initial characterization of the lipid headgroup labeled Gd(III)-microbubbles by MRI revealed that the Gd(III) relaxivity increased after microbubble fragmentation into non-gas-containing lipid vesicles. This behavior was explained to stem from an increase in interaction between water protons and the Gd(III)-bound lipid fragments due to an increase in lipid headgroup area after microbubble fragmentation. To explore this hypothesis, an alternative construct consisting of Gd(III) preferentially bound to the protective poly(ethylene glycol) (PEG) brush of the lipid shell architecture was also designed and compared to the lipid headgroup-labeled Gd(III)-microbubbles. Nuclear magnetic resonance (NMR) analysis revealed that, in contrast to the headgroup labeled Gd(III)-microbubbles, the relaxivity of the PEG-labeled Gd(III)-microbubbles decreased after microbubble fragmentation. NMR analysis also revealed an independent concentration-dependent enhancement of the transverse MR signal by virtue of the microbubble gas core. The results of this study illustrated the roles that Gd(III) placement on the lipid shell and the presence of the gas core may play on the MR signal when monitoring Gd(III)-microbubble cavitation during non-invasive surgery with FUS.Biomedical engineering, Chemical engineeringjaf2147Chemical EngineeringDissertationsMagnetic Resonance Imaging Applications of Pseudo-Random Amplitude Modulationhttp://academiccommons.columbia.edu/catalog/ac:175415
Zou, Xiaoweihttp://dx.doi.org/10.7916/D8PZ56ZTMon, 07 Jul 2014 00:00:00 +0000Magnetic resonance imaging (MRI) is a medical imaging technique which can provide fine tissue contrast with relatively high image resolution in human. Besides the image quality, imaging speed is the other major concern in modern MRI, especially in human experiments where sufficient volumetric coverage is necessary. One approach to increase imaging speed is increasing image acquisition speed so that the same amount of volumetric coverage can be achieved within shorter time under conventional experiment paradigms. In this dissertation, the application of pseudo-random amplitude modulation (PRAM) in MRI was explored to increase imaging speed by designing more efficient experiment paradigms for the human brain. Two relatively slow MRI studies were investigated. The first study was measuring longitudinal relaxation time. A novel method "Relaxation by Amplitude Modulation" (RLXAM) was invented. The RLXAM modulation code can be chosen from a large family of binary sequences. PRAM is a specific implementation using the maximum length sequence, also known as pseudo-random sequence. The other study was measuring transit time distribution in arterial spin labeling. The application of PRAM in transit time measurement was reported before on a 3T Philips Acheiva scanner using a single-slice protocol with standard gradient echo acquisition. The original theory was extended and multi-slice sequences with two different acquisition strategies were developed on a 3T Siemens Trio scanner. Both methods were applied to both phantom and human to demonstrate the theories and evaluate their performance.Biomedical engineeringBiomedical EngineeringDissertationsTowards Clinical Use of Engineered Tissues for Cartilage Repairhttp://academiccommons.columbia.edu/catalog/ac:175507
Tan, Andreahttp://dx.doi.org/10.7916/D8319T13Mon, 07 Jul 2014 00:00:00 +0000Osteoarthritis (OA), the most prevalent form of joint disease, afflicts nine percent of the US population over the age of thirty and costs the economy nearly $100 billion annually in healthcare and socioeconomic costs. It is characterized by joint pain and dysfunction, though the pathophysiology remains largely unknown. The progressive loss of cartilage followed by inadequate repair and remodeling of subchondral bone are common hallmarks of this degenerative disease. Due to its avascular nature and limited cellularity, articular cartilage exhibits a poor intrinsic healing response following injury. As such, significant research efforts are aimed at producing engineered cartilage as a cell-based approach for articular cartilage repair. However, the knee joint is mechanically demanding, and during injury, also a milieu of harsh inflammatory agents. The unforgiving mechanochemical environment requires constructs that are capable of bearing such burdens. To this end, previous work in our laboratory has explored the application of stimuli inspired by the native joint environment in attempts to create tissue with functional properties similar to native cartilage so that it may restore loading to the joint. While we have had success at producing these replacement tissues, there is little evidence in the literature that the biological functionality (i.e. response to in vivo-like conditions) of engineered cartilage matches native cartilage. Therefore, in an effort to provide a more complete characterization of the functional nature of developing tissues and facilitate their use clinically, the overarching motivation of the work described in this dissertation is two-fold: 1) characterize the response of engineered cartilage to chemical and mechanical injury; and 2) develop strategies for enhancing the performance and protection of engineered cartilage for in vivo success. Studies in the literature have extensively characterized the effects of wounding to native articular cartilage as well as the effects of an inflammatory environment. For mechanical injuries, cell death is immediate and progressive, ultimately leading to failure of the tissue. Chemical insult has been shown to promote degradation of the matrix components, also leading to failure of the tissue. Under a controlled application of injury (mechanical and chemical), it was found that engineered cartilage, in contrast to native cartilage, has the potential to repair itself following an injury event, as long as there is no catastrophic damage to the matrix. Additionally, when this matrix is intact and well-developed, engineered cartilage constructs exhibit a resistance to degradation, highlighting the potential utility of engineered cartilage as replacement tissues. Enhancing functionality in engineered cartilage was also explored, with the aim of developing strategies to improve, repair, and protect engineered cartilage constructs for their use in vivo. For these purposes, the studies in this dissertation spanned both 2D migration studies to influence the limited wound repair potential of cells as well as 3D culture studies to explore the possibility of protection effects at a tissue level. Together, these models allowed us to capture the complexity needed to fully develop approaches for cartilage repair. Though it has previously been found that applied DC electric fields modulate cell migration, we have developed a novel strategy of employing this technique to screen for desirable populations of cells (those with the greatest capacity for directed migration) to use in cartilage repair. We also found that the AQP1 water channel plays a key role in mechanosensing the extracellular environment, highlighting the potential for its use in therapeutic strategies. For tissue engineering efforts at creating functional cartilage replacement, we uncovered novel strategies to foster better tissue development via co-culture systems and promote the resistance of engineered cartilage to catabolic factors. These findings motivate their potential use in therapeutics and in tissue engineering efforts at creating clinically relevant tissue-engineered constructs for the treatment of OA or following injury. The research described in this dissertation has characterized the biological functionality of engineered tissues and identified strategies for enhancing their use in vivo by modulating the subsequent response to injury, laying the foundation for their use in clinical applications.Biomedical engineeringart2122Biomedical EngineeringDissertationsDevelopment of a Vascular Optical Tomographic Imaging System for the Diagnosis and Monitoring of Peripheral Arterial Diseasehttp://academiccommons.columbia.edu/catalog/ac:175436
Khalil, Michaelhttp://dx.doi.org/10.7916/D8DF6PCQMon, 07 Jul 2014 00:00:00 +0000The overall goal of this dissertation is to describe the development of a dynamic diffuse optical tomographic (DDOT) imaging system for the diagnosis and monitoring of peripheral arterial disease (PAD) within the lower extremities. PAD affects 8-12 million individuals in the United States and is associated with significant morbidity and mortality. Early detection and monitoring of disease progression is crucial, but remains difficult. This is especially true for diabetic patients, as roughly 30 percent of all diabetic patients over the age of 50 are diagnosed with PAD. Diabetic patients have calcified arteries, which renders them incompressible. This falsely elevates blood pressure readings and causes false negative readings using traditional diagnostic techniques. DDOT offers an attractive opportunity to overcome current shortcomings in assessing PAD. This technology uses harmless near-infrared light to create three-dimensional, time-dependent images of biological tissues. Using DDOT to measure blood-perfusion in the foot should help diagnose and monitor the PAD. To test this hypothesis, I adapted an existing optical tomographic imaging system for the particular application of vascular imaging in the foot. In particular I design and tested various measuring probes that can accommodate different foot sizes and shapes. The result was a patient friendly interface that can be employed in a clinical setting. Using this modified DDOT imager, which we called vascular optical tomographic imaging (VOTI) system, I conducted a 40-subject pilot study to quantify its ability to diagnose PAD. The subjects were recruited into three cohorts, non-diabetic PAD patients (N=10), PAD Patients (N=10) and healthy volunteers (N=20). With this data in hand, I performed a comprehensive data analysis, in which I found imaging features that led to a good separation between the healthy and affected cohorts. In particular I demonstrated that statistically significant difference exist between the amount of blood pooling in the leg during a 1-minute, 60mmHg thigh cuff occlusion within healthy subjects and both affected cohorts (P=0.006, P=0.006). In addition, using receiver operating characteristic (ROC) curve analysis, I identified that the new VOTI system could diagnose PAD with a sensitivity and specificity of over 80%, even within the diabetic patients. This imaging modality was also capable of identifying the severity of the disease with similar accuracy to the existing diagnostic methods while not being inhibited by arterial calcifications. Furthermore, the VOTI system provided spatial information, helping identify which regions of the foot suffered from mal-perfusion. When combined with angiosome theory, the spatial information could help physicians in deciding how to intervene in PAD patients. After completing this first clinical study, I developed a dedicated VOTI system by entirely redesigning the hard and software. This new system has many novelties over its predecessor. First it employs a contact-free patient interface that allows to imaging patients with ulcerations. The illumination fibers used do not need to make physical contact with the patient. Second, instead of using individual silicon photodiodes as detectors, a highly sensitive CCD camera is use to detect transmitted light intensity. The system has two wavelengths of light (660 and 860 nm), which can be illuminated at up to 20 different positions along the surface of the foot. The system is built for dynamic imaging and is capable of imaging at a multispectral-volumetric frame rate speeds of 1 Hz. This set-up allows us to create three-dimensional images of large portions of the foot. This imaging system was tested on phantom studies and healthy volunteers and was shown to be able to image blood flow dynamics within a three-dimensional volume of the foot.Biomedical engineeringBiomedical EngineeringDissertationsInnate Immune-Like Function of Osteogenic Cells and Their Effects on Inflammatory Osteolysishttp://academiccommons.columbia.edu/catalog/ac:175738
Lee, Heon Goohttp://dx.doi.org/10.7916/D8MP51FNMon, 07 Jul 2014 00:00:00 +0000The immune response is an essential defense mechanism that protects the human body from foreign infection. Nevertheless, excessive immune response results in high levels of inflammation leading to destruction of healthy tissues. In orthopaedic fields, this duality of the immune response has been a challenge to the success of arthroplasties. Wear particle-induced inflammatory osteolysis is considered a major culprit of implant failure. Resident osteogenic bone cells, such as osteoprogenitors and osteoblasts, are exposed to wear particles. Although osteogenic cells are responsible for the initial osseointegration of implants and ongoing bone regeneration, their response to wear particles has been underestimated. Thus, the goal of this dissertation is to explore the immune mechanisms of osteogenic cells and to identify the role of osteogenic cells in particle mediated osteolysis. To meet this end, we evaluated the immune capacity of osteogenic cells by exploring their ability to phagocytose wear particles and subsequently express pro-inflammatory cytokines. We developed a customized JAVA program and confocal microscopy methodology to quantify the phagocytic activity of osteogenic cells. Osteoprogenitors and osteoblasts were able to phagocytose Titanium (Ti) particles with aggressive actin remodeling. The actin remodeling to engulf particles activated ERK-CEBP/b pathway leading to Cox2 and IL6 gene expression. Interestingly, equibiaxial strain also increased inflammatory gene expression such as MCSF, IL6, and Cox2 through the ERK pathway. Physiological and super-physiological levels of strain were applied to osteogenic cells and macrophage-like cells via Flexcell system. Super-physiological strain exaggerated Ti particle induced inflammatory gene expression from osteogenic cells, while macrophage-like cells were not affected by strain. Taken together, these data suggest actin and ERK-CEBP/b signaling mediates phagocytosis-induced innate immune responses of osteogenic cells. Next, we confirmed the role of osteogenic cells in inflammatory osteolysis. Although we observed that osteogenic cells secrete inflammatory cytokines after phagocytosis of wear particles, it was difficult to discern whether osteogenic cells have a major role in inflammatory osteolysis because there are a multitude of cells exposed to wear particles at the site of bone implant. Thus, we developed an osteogenic cell line specific ERK-dysfunctional mouse using an osterix-promoter-driven CRE-loxp system (CRE/dn-MEK1). An in vivo mouse calvaria model was utilized to induce inflammatory osteolysis. Ti particles were implanted on top of pericranium layer without invasive incision. This approach allowed observation of osteogenic cell responses to Ti particles in the pericranium. With this model, we observed severe calvarial osteolysis with increased osteoclastogenesis and pro-inflammatory cytokine release of IL6, PGE2 and MCSF. Significantly decreased inflammatory cytokine release and macrophage migration were observed in the CRE/dn-MEK1 mouse in in vivo mouse calvaria model and in vitro experiments. Similar trends were detected in mouse calvaria treated with AZD6244, a potent ATP-uncompetitive inhibitor of MAPK/ERK kinase. In summary, this study supports hypothesis that (1) osteogenic cells are able to initiate inflammatory responses through well established innate immune function and (2) the ERK pathway could be a clinically important therapeutic target for preventing inflammatory osteolysis.Biomedical engineering, Biology, MedicineOrthopaedic Surgery, Biomedical EngineeringDissertationsNeural and Ocular Signals Evoked by Visual Targets in Naturalistic Environmentshttp://academiccommons.columbia.edu/catalog/ac:176101
Jangraw, Davidhttp://dx.doi.org/10.7916/D8DN436RMon, 07 Jul 2014 00:00:00 +0000This dissertation will use neural imaging, eye-tracking, machine learning, and system development to elucidate the process of visual decision-making in environments that simulate important elements of a human's natural experience. This "naturalistic visual decision-making" represents a relatively unexplored space in neuroscience: while the simplest reductions of visual decision-making are well studied, many of the complexities of natural environments - rich visual scenes, dynamic views, and subject agency - are absent in all but a few experiments. In this dissertation, we first characterize the effects of discrete evidence accumulation, an important element of processing complex stimuli, on visual decision-making. Next, we construct an experimental design environment to facilitate controlled studies of naturalistic visual decision-making. Finally, we develop a system that can apply our newfound understanding of naturalistic visual decision-making, test it in the experimental design environment, and leverage it into a practical BCI system. Taken together, these studies explore new avenues in neuroscience, machine learning, and application development.Biomedical engineering, Neurosciencesdcj2110Biomedical EngineeringDissertationsModeling Nanoscale Transport Systemshttp://academiccommons.columbia.edu/catalog/ac:175900
Idan, Oferhttp://dx.doi.org/10.7916/D8DZ06FQMon, 07 Jul 2014 00:00:00 +0000Mathematical formulation and physical models are the foundation of scientific understanding and technological advancement. Our ability to design experiments effectively is heavily dependent on our physical understanding of the system under investigation, and careful mathematical analysis is required in order to effectively progress from scientific concepts towards viable technologies. With increasing system complexity, the focus of mathematical formulation has shifted from simple, elegant models which rely on basic physical concepts to tailored, increasingly complex solutions using high-powered simulations and numerical solutions. While these methods may provide insights into specific systems, adapting these models to different systems is generally difficult, even when the systems under question operate according to the same physical laws. This is especially evident in nanobiotechnology, where the complexity of the systems studied has given rise to experiment-driven focus. Our aim is to focus on the mathematical modeling of transport processes in nanoscale systems, and to construct generalized, conceptual models for three model systems, which in turn could be applied to many biological and engineered systems. The three model systems we use - enzyme cascades, coupled molecular motors and self-assembling molecular shuttles provide a broad basis for generalized transport systems in nanoscale systems. These systems combine diffusive and active transport, as well as diverse assembly conditions and multi-scale systems with size scales spanning nano- to millimeter sizes and system complexity ranging from isolated two-component systems to multimolecular, highly-coupled systems. By applying and adapting these basic models to increasingly complex systems, we can both understand the physics behind nanoscale systems, as well as design these systems with increased robustness, scalability and repeatability.Biomedical engineeringBiomedical EngineeringDissertationsSimultaneous EEG-fMRI Reveals Temporal Evolution of Coupling between Supramodal Cortical Attention Networks and the Brainstemhttp://academiccommons.columbia.edu/catalog/ac:174864
Walz, Jennifer Marie; Goldman, Robin I.; Carapezza, Michael; Muraskin, Jordan Scott; Brown, Truman R.; Sajda, Paulhttp://dx.doi.org/10.7916/D8FT8J4SMon, 19 May 2014 00:00:00 +0000Cortical and subcortical networks have been identified that are commonly associated with attention and task engagement, along with theories regarding their functional interaction. However, a link between these systems has not yet been demonstrated in healthy humans, primarily because of data acquisition and analysis limitations. We recorded simultaneous EEG–fMRI while subjects performed auditory and visual oddball tasks and used these data to investigate the BOLD correlates of single-trial EEG variability at latencies spanning the trial. We focused on variability along task-relevant dimensions in the EEG for identical stimuli and then combined auditory and visual data at the subject level to spatially and temporally localize brain regions involved in endogenous attentional modulations. Specifically, we found that anterior cingulate cortex (ACC) correlates strongly with both early and late EEG components, whereas brainstem, right middle frontal gyrus (rMFG), and right orbitofrontal cortex (rOFC) correlate significantly only with late components. By orthogonalizing with respect to event-related activity, we found that variability in insula and temporoparietal junction is reflected in reaction time variability, rOFC and brainstem correlate with residual EEG variability, and ACC and rMFG are significantly correlated with both. To investigate interactions between these correlates of temporally specific EEG variability, we performed dynamic causal modeling (DCM) on the fMRI data. We found strong evidence for reciprocal effective connections between the brainstem and cortical regions. Our results support the adaptive gain theory of locus ceruleus–norepinephrine (LC–NE) function and the proposed functional relationship between the LC–NE system, right-hemisphere ventral attention network, and P300 EEG response.Biomedical engineering, Neurosciencesjw2552, jsm2112, trb11, ps629Radiology, Biomedical EngineeringArticlesCorrelated Components of Ongoing EEG Point to Emotionally Laden Attention – a Possible Marker of Engagement?http://academiccommons.columbia.edu/catalog/ac:174011
Dmochowski, Jacek P.; Sajda, Paul; Dias, Joao; Parra, Lucas C.http://dx.doi.org/10.7916/D84J0C61Mon, 19 May 2014 00:00:00 +0000Recent evidence from functional magnetic resonance imaging suggests that cortical hemodynamic responses coincide in different subjects experiencing a common naturalistic stimulus. Here we utilize neural responses in the electroencephalogram (EEG) evoked by multiple presentations of short film clips to index brain states marked by high levels of correlation within and across subjects. We formulate a novel signal decomposition method which extracts maximally correlated signal components from multiple EEG records. The resulting components capture correlations down to a one-second time resolution, thus revealing that peak correlations of neural activity across viewings can occur in remarkable correspondence with arousing moments of the film. Moreover, a significant reduction in neural correlation occurs upon a second viewing of the film or when the narrative is disrupted by presenting its scenes scrambled in time. We also probe oscillatory brain activity during periods of heightened correlation, and observe during such times a significant increase in the theta band for a frontal component and reductions in the alpha and beta frequency bands for parietal and occipital components. Low-resolution EEG tomography of these components suggests that the correlated neural activity is consistent with sources in the cingulate and orbitofrontal cortices. Put together, these results suggest that the observed synchrony reflects attention- and emotion-modulated cortical processing which may be decoded with high temporal resolution by extracting maximally correlated components of neural activity.Biomedical engineering, Bioinformatics, Neurosciencesps629Biomedical EngineeringArticlesYou Can’t Think and Hit at the Same Time: Neural Correlates of Baseball Pitch Classificationhttp://academiccommons.columbia.edu/catalog/ac:174025
Sherwin, Jason Samuel; Muraskin, Jordan Scott; Sajda, Paulhttp://dx.doi.org/10.7916/D8GQ6VVFMon, 19 May 2014 00:00:00 +0000Hitting a baseball is often described as the most difficult thing to do in sports. A key aptitude of a good hitter is the ability to determine which pitch is coming. This rapid decision requires the batter to make a judgment in a fraction of a second based largely on the trajectory and spin of the ball. When does this decision occur relative to the ball’s trajectory and is it possible to identify neural correlates that represent how the decision evolves over a split second? Using single-trial analysis of electroencephalography (EEG) we address this question within the context of subjects discriminating three types of pitches (fastball, curveball, slider) based on pitch trajectories. We find clear neural signatures of pitch classification and, using signal detection theory, we identify the times of discrimination on a trial-to-trial basis. Based on these neural signatures we estimate neural discrimination distributions as a function of the distance the ball is from the plate. We find all three pitches yield unique distributions, namely the timing of the discriminating neural signatures relative to the position of the ball in its trajectory. For instance, fastballs are discriminated at the earliest points in their trajectory, relative to the two other pitches, which is consistent with the need for some constant time to generate and execute the motor plan for the swing (or inhibition of the swing). We also find incorrect discrimination of a pitch (errors) yields neural sources in Brodmann Area 10, which has been implicated in prospective memory, recall, and task difficulty. In summary, we show that single-trial analysis of EEG yields informative distributions of the relative point in a baseball’s trajectory when the batter makes a decision on which pitch is coming.Biomedical engineering, Neurosciences, Bioinformaticsjss2212, jsm2112, ps629Biomedical EngineeringArticlesPost-stimulus Endogenous and Exogenous Oscillations Are Differentially Modulated by Task Difficultyhttp://academiccommons.columbia.edu/catalog/ac:174003
Li, Yun; Lou, Bin; Gao, Xiaorong; Sajda, Paulhttp://dx.doi.org/10.7916/D8862DKXMon, 19 May 2014 00:00:00 +0000We investigate the modulation of post-stimulus endogenous and exogenous oscillations when a visual discrimination is made more difficult. We use exogenous frequency tagging to induce steady-state visually evoked potentials (SSVEP) while subjects perform a face-car discrimination task, the difficulty of which varies on a trial-to-trial basis by varying the noise (phase coherence) in the image. We simultaneously analyze amplitude modulations of the SSVEP and endogenous alpha activity as a function of task difficulty. SSVEP modulation can be viewed as a neural marker of attention toward/away from the primary task, while modulation of post-stimulus alpha is closely related to cortical information processing. We find that as the task becomes more difficult, the amplitude of SSVEP decreases significantly, approximately 250–450 ms post-stimulus. Significant changes in endogenous alpha amplitude follow SSVEP modulation, occurring at approximately 400–700 ms post-stimulus and, unlike the SSVEP, the alpha amplitude is increasingly suppressed as the task becomes less difficult. Our results demonstrate simultaneous measurement of endogenous and exogenous oscillations that are modulated by task difficulty, and that the specific timing of these modulations likely reflects underlying information processing flow during perceptual decision-making.Biomedical engineering, Bioinformatics, Neurosciencesbl2372, ps629Biomedical EngineeringArticlesIntermediate-Level Visual Representations and the Construction of Surface Perceptionhttp://academiccommons.columbia.edu/catalog/ac:174045
Sajda, Paul; Finkel, Leif H.http://dx.doi.org/10.7916/D8Q81B52Mon, 19 May 2014 00:00:00 +0000Visual processing has often been divided into three stages—early, intermediate, and high level vision, which roughly correspond to the sensation, perception, and cognition of the visual world. In this paper, we present a network-based model of intermediate-level vision that focuses on how surfaces might be represented in visual cortex. We propose a mechanism for representing surfaces through the establishment of “ownership”—a selective binding of contours and regions. The representation of ownership provides a central locus for visual integration. Our simulations show the ability to segment real and illusory images in a manner consistent with human perception. In addition, through ownership, other processes such as depth, transparency, and surface completion can interact with one another to organize an image into a perceptual scene.Biomedical engineering, Neurosciences, Psychologyps629Biomedical EngineeringArticlesEEG-Informed fMRI Reveals Spatiotemporal Characteristics of Perceptual Decision Makinghttp://academiccommons.columbia.edu/catalog/ac:174060
Philiastides, Marios G.; Sajda, Paulhttp://dx.doi.org/10.7916/D8B27SDCMon, 19 May 2014 00:00:00 +0000Single-unit and multiunit recordings in primates have already established that decision making involves at least two general stages of neural processing: representation of evidence from early sensory areas and accumulation of evidence to a decision threshold from decision-related regions. However, the relay of information from early sensory to decision areas, such that the accumulation process is instigated, is not well understood. Using a cued paradigm and single-trial analysis of electroencephalography (EEG), we previously reported on temporally specific components related to perceptual decision making. Here, we use information derived from our previous EEG recordings to inform the analysis of fMRI data collected for the same behavioral task to ascertain the cortical origins of each of these EEG components. We demonstrate that a cascade of events associated with perceptual decision making takes place in a highly distributed neural network. Of particular importance is an activation in the lateral occipital complex implicating perceptual persistence as a mechanism by which object decision making in the human brain is instigated.Biomedical engineering, Neurosciences, Psychologyps629Biomedical EngineeringArticlesPerceptual Decision Making “Through the Eyes” of a Large-scale Neural Model of V1http://academiccommons.columbia.edu/catalog/ac:174032
Shi, Jianing V.; Wielaard, Jim; Smith, R. Theodore; Sajda, Paulhttp://dx.doi.org/10.7916/D83J3B33Mon, 19 May 2014 00:00:00 +0000Sparse coding has been posited as an efficient information processing strategy employed by sensory systems, particularly visual cortex. Substantial theoretical and experimental work has focused on the issue of sparse encoding, namely how the early visual system maps the scene into a sparse representation. In this paper we investigate the complementary issue of sparse decoding, for example given activity generated by a realistic mapping of the visual scene to neuronal spike trains, how do downstream neurons best utilize this representation to generate a “decision.” Specifically we consider both sparse (L1-regularized) and non-sparse (L2 regularized) linear decoding for mapping the neural dynamics of a large-scale spiking neuron model of primary visual cortex (V1) to a two alternative forced choice (2-AFC) perceptual decision. We show that while both sparse and non-sparse linear decoding yield discrimination results quantitatively consistent with human psychophysics, sparse linear decoding is more efficient in terms of the number of selected informative dimension.Biomedical engineering, Neurosciences, Psychologyrts1, ps629Biomedical EngineeringArticlesNeural Representation of Task Difficulty and Decision Making during Perceptual Categorization: A Timing Diagramhttp://academiccommons.columbia.edu/catalog/ac:174064
Philiastides, Marios G.; Ratcliff, Roger; Sajda, Paulhttp://dx.doi.org/10.7916/D82J6905Mon, 19 May 2014 00:00:00 +0000When does the brain know that a decision is difficult to make? How does decision difficulty affect the allocation of neural resources and timing of constituent cortical processing? Here, we use single-trial analysis of electroencephalography (EEG) to identify neural correlates of decision difficulty and relate these to neural correlates of decision accuracy. Using a cued paradigm, we show that we can identify a component in the EEG that reflects the inherent task difficulty and not simply a correlation with the stimulus. We find that this decision difficulty component arises ≈220 ms after stimulus presentation, between two EEG components that are predictive of decision accuracy [an “early” (170 ms) and a “late” (≈300 ms) component]. We use these results to develop a timing diagram for perceptual decision making and relate the component activities to parameters of a diffusion model for decision making.Biomedical engineering, Neurosciences, Psychologyps629Biomedical EngineeringArticlesComparing Neural Correlates of Visual Target Detection in Serial Visual Presentations Having Different Temporal Correlationshttp://academiccommons.columbia.edu/catalog/ac:174017
Luo, An; Sajda, Paulhttp://dx.doi.org/10.7916/D8W0941MMon, 19 May 2014 00:00:00 +0000Most visual stimuli we experience on a day-to-day basis are continuous sequences, with spatial structure highly correlated in time. During rapid serial visual presentation (RSVP), this correlation is absent. Here we study how subjects’ target detection responses, both behavioral and electrophysiological, differ between continuous serial visual sequences (CSVP), flashed serial visual presentation (FSVP) and RSVP. Behavioral results show longer reaction times for CSVP compared to the FSVP and RSVP conditions, as well as a difference in miss rate between RSVP and the other two conditions. Using mutual information, we measure electrophysiological differences in the electroencephalography (EEG) for these three conditions. We find two peaks in the mutual information between EEG and stimulus class (target vs. distractor), with the second peak occurring 30–40 ms earlier for the FSVP and RSVP conditions. In addition, we find differences in the persistence of the peak mutual information between FSVP and RSVP conditions. We further investigate these differences using a mutual information based functional connectivity analysis and find significant fronto-parietal functional coupling for RSVP and FSVP but no significant coupling for the CSVP condition. We discuss these findings within the context of attentional engagement, evidence accumulation and short-term visual memory.Biomedical engineering, Bioinformatics, Neurosciencesps629Biomedical EngineeringArticlesFast Bootstrapping and Permutation Testing for Assessing Reproducibility and Interpretability of Multivariate fMRI Decoding Modelshttp://academiccommons.columbia.edu/catalog/ac:174074
Conroy, Bryan R.; Walz, Jennifer Marie; Sajda, Paulhttp://dx.doi.org/10.7916/D8JM27Q8Mon, 19 May 2014 00:00:00 +0000Multivariate decoding models are increasingly being applied to functional magnetic imaging (fMRI) data to interpret the distributed neural activity in the human brain. These models are typically formulated to optimize an objective function that maximizes decoding accuracy. For decoding models trained on full-brain data, this can result in multiple models that yield the same classification accuracy, though some may be more reproducible than others—i.e. small changes to the training set may result in very different voxels being selected. This issue of reproducibility can be partially controlled by regularizing the decoding model. Regularization, along with the cross-validation used to estimate decoding accuracy, typically requires retraining many (often on the order of thousands) of related decoding models. In this paper we describe an approach that uses a combination of bootstrapping and permutation testing to construct both a measure of cross-validated prediction accuracy and model reproducibility of the learned brain maps. This requires re-training our classification method on many re-sampled versions of the fMRI data. Given the size of fMRI datasets, this is normally a time-consuming process. Our approach leverages an algorithm called fast simultaneous training of generalized linear models (FaSTGLZ) to create a family of classifiers in the space of accuracy vs. reproducibility. The convex hull of this family of classifiers can be used to identify a subset of Pareto optimal classifiers, with a single-optimal classifier selectable based on the relative cost of accuracy vs. reproducibility. We demonstrate our approach using full-brain analysis of elastic-net classifiers trained to discriminate stimulus type in an auditory and visual oddball event-related fMRI design. Our approach and results argue for a computational approach to fMRI decoding models in which the value of the interpretation of the decoding model ultimately depends upon optimizing a joint space of accuracy and reproducibility.Biomedical engineering, Neurosciencesbc2468, jw2552, ps629Biomedical EngineeringArticlesObject Discrimination Based on Depth-from-Occlusionhttp://academiccommons.columbia.edu/catalog/ac:174070
Finkel, Leif H.; Sajda, Paulhttp://dx.doi.org/10.7916/D8T151R0Mon, 19 May 2014 00:00:00 +0000We present a model of how objects can be visually discriminated based on the extraction of depth-from-occlusion. Object discrimination requires consideration of both the binding problem and the problem of segmentation. We propose that the visual system binds contours and surfaces by identifying "proto-objects"-compact regions bounded by contours. Proto-objects can then be linked into larger structures. The model is simulated by a system of interconnected neural networks. The networks have biologically motivated architectures and utilize a distributed representation of depth. We present simulations that demonstrate three robust psychophysical properties of the system. The networks are able to stratify multiple occluding objects in a complex scene into separate depth planes. They bind the contours and surfaces of occluded objects (for example, if a tree branch partially occludes the moon, the two "half-moons" are bound into a single object). Finally, the model accounts for human perceptions of illusory contour stimuli.Biomedical engineering, Neurosciences, Psychologyps629Biomedical EngineeringArticlesAdaptive Thresholding for Improving Sensitivity in Single-trial Simultaneous EEG/fMRIhttp://academiccommons.columbia.edu/catalog/ac:174038
deBettencourt, Megan; Goldman, Robin; Brown, Truman R.; Sajda, Paulhttp://dx.doi.org/10.7916/D8V122WCMon, 19 May 2014 00:00:00 +0000A common approach used to fuse simultaneously recorded EEG and fMRI is to correlate trial-by-trial variability in the EEG, or variability of components derived therefrom, with the blood oxygenation level dependent response. When this correlation is done using the conventional univariate approach, for example with the general linear model, there is the usual problem of correcting the statistics for multiple comparisons. Cluster thresholding is often used as the correction of choice, though in many cases it is utilized in an ad hoc way, for example by employing the same cluster thresholds for both traditional regressors (stimulus or behaviorally derived) and EEG-derived regressors. In this paper we describe a resampling procedure that takes into account the a priori statistics of the trial-to-trial variability of the EEG-derived regressors in a way that trades off cluster size and maximum voxel Z-score to properly correct for multiple comparisons. We show that this data adaptive procedure improves sensitivity for smaller clusters of activation, without sacrificing the specificity of the results. Our results suggest that extra care is needed in correcting statistics when the regressor model is derived from noisy and/or uncertain measurements, as is the case for regressors constructed from single-trial variations in the EEG.Biomedical engineering, Neurosciences, Psychologytrb11, ps629Radiology, Biomedical EngineeringArticlesRoles of Cell Junctions and the Cytoskeleton in Substrate-free Cell Sheet Engineeringhttp://academiccommons.columbia.edu/catalog/ac:173862
Wei, Qihttp://dx.doi.org/10.7916/D8MP51D6Wed, 14 May 2014 00:00:00 +0000In multicellular organisms, one-cell-thick monolayer sheets are the simplest tissues, yet they play crucial roles in physiology and tissue engineering. Cells within these sheets are tightly connected to each other through specialized cell-adhesion molecules that typically cluster into in discrete patches called cell-cell junctions. Working together, these junctional organelles glue cells to their neighbors, integrate the cytoskeletons into a mechanical syncytium and transduce a variety of mechanical signals. Human bodies offer many vivid illustration of how a cell sheet physiology changes considerably during development and diseases, as shown in epidermal blistering and certain cardiomyopathy. Despite the extensive molecular and clinical work on cell junctions, relevant in vitro experimental data are often masked by cell-substrate interactions due to a lack of suitable experimental methods. It is therefore important to develop novel in vitro methods for characterizing how junctional proteins, as well as tightly associated cytoskeletal proteins, may modulate various cellular behaviors, such as viability and apoptosis, cell-cell adhesiveness and tissue integrity. Control over cell viability is a fundamental property underlying numerous physiological processes. Cell-cell contact is likely to play a significant role in regulating cell vitality, but its function is easily masked by cell-substrate interactions, thus remains incompletely characterized. In the first part of this thesis, we developed an enzyme-based whole cell sheet lifting method and generated substrate- and scaffold-free keratinocyte (N/TERT-1) cell sheets. Cells within the suspended cell sheets have persisting intercellular contacts and remain viable, in contrast to trypsinized cells suspended without either cell-cell or cell-substrate contact, which underwent apoptosis at high rates. Suppression of junctional protein plakoglobin weakened cell-cell adhesion in cell sheets and suppressed apoptosis in suspended, trypsinized cells. These results demonstrate that cell-cell contact may be a fundamental control mechanism governing cell viability and that the plakoglobin is a key regulator of this process. The study also laid groundwork for subsequent characterization and manipulation of viable cell sheets for cell sheet engineering purpose. Cell sheet engineering, characterized by harvest of cultured cell monolayer as a scaffold-free sheet, was recently developed. Particularly, cell sheet engineering based cardiac tissue engineering has emerged as an alternative method for the repair of damaged heart tissue. Such an engineered cell sheet offers a new way to study cell junctions when substrate interactions are no longer dominant. While this method is promising, it is limited by the fragility and shrinkage of the sheets as well as the lack of information regarding the characteristics of such sheets. In next part of the thesis we pursued two related research projects by developing a novel partial-lift method to generate strong, unshrunk substrate-free and scaffold-free cell sheets, first using skin cells and then refined and expanded to cardiac cells. The rationales for this approach are the ease with which skin cells can be manipulated, the similarities in cell junctions between skin and cardiac cells, and their potential clinical applications. These partially-lifted cell sheets engage primarily in cell-cell interactions, yet are amenable to biological and chemical perturbations and, importantly, mechanical conditioning. This simple yet powerful method was then deployed to test the hypothesis that the lifted cells would exhibit substantial reinforcement of key cytoskeletal and junctional components at cell-cell contacts, and that such reinforcement would be enhanced by mechanical conditioning. Results further demonstrate that the mechanical strength and cohesion of the substrate-free cell sheets strongly depend on the integrity of the actomyosin cytoskeleton and expression of the junctional protein plakoglobin. Moreover, our results showed that dissociating cell-substrate interactions and implementing mechanical conditioning enhances contraction, calcium signaling, alters viscoelastic property, and thus improves the functional cell-cell coupling in the cardiac sheets. In sum, this thesis represents a first systematic examination of junctional regulation of cell viability and mechanical conditioning on cells with primarily cell-cell interactions. The information gained from this study will help advance our understanding of cell-cell interactions and improve cell sheets biomechanical properties. For tissue engineering purposes, our dispase-based partial-lift cell sheet harvesting method has the advantage of being biocompatible, easily applicable, rapidly collectable and stretchable, compared to currently available techniques. This simple yet powerful partial lift technique has enormous potential for fabricating clinically applicable skin and cardiac tissues.Biomedical engineeringqw2133Biomedical EngineeringDissertationsPyrintegrin Induced Adipogenesis: Biology, Bioengineering and Therapeuticshttp://academiccommons.columbia.edu/catalog/ac:174633
Shah, Bhrantihttp://dx.doi.org/10.7916/D8MK6B0WTue, 15 Apr 2014 00:00:00 +0000Adipose tissue is traditionally regarded as a source of energy storage and cushion for skeletal functions. Soft tissue injuries take place in war and peace time, as a result of tumor resection such as breast cancer, and in rare disorders such as lipoatrophy. Adipose tissue reconstruction is one of the key challenges in medicine. Here we report the robust differentiation of human adipose derived stem cells using a small molecule into adipocytes. This thesis describes the biological effects and actions of novel unknown small-molecule inhibitor of BMP signaling--Pyrintegrin, which was previously found to promote human embryonic stem cells survival. The overall objective of this thesis is to test the hypothesis that this novel drug, Pyrintegrin treatment will induce, promote and accelerate adipogenic differentiation of stem cells in vitro and in vivo. We found that Pyrintegrin promotes the adipogenesis-dependent transcriptional changes of multiple gene products involved in the adipogenic process, including peroxisome proliferator-activated receptor (PPARgamma), CCAAT/enhancer-binding protein alpha; (C/EBPalpha), adiponectin and leptin secretion, and total triglyceride secretion. When transplanted into mice, Pyrintegrin treated adipose cells/progenitors gave rise to ectopic fat pads with the morphological and functional characteristics of white adipose tissue. This was further confirmed by higher expression of human PPARgamma gene in Pyrintegrin treated cells group than any other group. We further tested the presence of human nuclear staining that confirmed the presence of human cells in all the transplanted groups. However, the number of positive human cells was substantially low in all the groups, which was likely due to transplanted cell death because of lack of vascularization. Hence, we further tested the Pyrintegrin adsorbed scaffolds capacity to regenerate better soft tissue compared to Ptn-free scaffold. We found that Ptn adsorbed scaffolds was positive for adipocytes as evident by positive Oil Red O staining. We further investigated the signaling mechanism of Pyrintegrin. Using a human PPARgamma reporter assay system, based on non-human mammalian cells engineered to express human PPARgamma protein, we found that Pyrintegrin is not a PPARgamma agonist as witnessed by lack of any luciferase activity. In contrast, Rosiglitazone, a known PPARgamma agonist demonstrated significant amount of luciferase activity in these reporter cells. We also found that Pyrintegrin selectively inhibits the BMP pathway and thus blocks BMP-mediated SMAD1/5 phosphorylation, target gene transcription and osteogenic differentiation. In vitro studies showed that Pyrintegrin inhibited the differentiation of stem cells into putative osteoblasts, as evident by decreased alizarin red staining. A striking finding was that Pyrintegrin up regulated markers of adipogenesis and stimulated lipid droplets accumulation in stem cells undergoing osteoblastic differentiation in vitro. This came at the expense of down regulating markers of osteogenesis and osteoblastic differentiation of stem cells, as compared to the cells undergoing osteogenic differentiation in the absence of the drug treatment. These findings show that the novel small-molecule Pyrintegrin is a potent promoter of adipogenesis and thus may have therapeutic potential for soft tissue reconstruction.Biomedical engineeringbs2315Biomedical EngineeringDissertationsElectromechanical Wave Imaginghttp://academiccommons.columbia.edu/catalog/ac:175194
Provost, Jeanhttp://dx.doi.org/10.7916/D83J3B2NTue, 15 Apr 2014 00:00:00 +0000Cardiac conduction abnormalities and arrhythmias are associated with stroke, heart failure, and sudden cardiac death, and remain a major cause of death and disability. However, the imaging tools currently available to the physician to guide these treatments by mapping the activation sequence of the heart are invasive, ionizing, time-consuming, and costly. In this dissertation, Electromechanical Wave Imaging (EWI) is described with an aim to characterize normal and abnormal rhythms noninvasively, transmurally, at the point of care, and in real time. More specifically, the methods to map the electromechanical wave (EW), i.e., the transient deformations occurring in response to the electrical activation of the heart, are developed and optimized. The correlation between EW and the electrical activation sequence during both normal and abnormal rhythms is demonstrated in canines in vivo and in silico. Finally, EWI is shown to noninvasively detect and characterize arrhythmias and conduction disorders in humans. Novel ultrasound imaging methodologies were developed to track the EW. Radio-frequency (RF) frames acquired at high frame rates were used in conjunction with cross-correlation algorithms to map the onset of the small, localized, transient deformations resulting from the electrical activation and forming the EW. To validate the capability of the EW to characterize cardiac rhythm, it was compared against the electrical activation in vivo and in silico. A high correlation between the electrical and electromechanical activations was obtained in normal canines in vivo during various pacing schemes and sinus rhythm. An in vivo-in silico framework was also developed to demonstrate that this correlation is maintained transmurally and independently of the imaging angle. EWI was also validated in abnormal canine hearts in vivo during ischemia, left bundle branch block, or atrio-ventricular dissociation. In a clinical feasibility study, we demonstrated that EWI was capable of noninvasively mapping normal and abnormal activation patterns in all four cardiac chambers of human subjects using a readily available clinical ultrasound scanner. Specifically, EWI maps were generated for three heart failure patients with cardiac resynchronization therapy (CRT) devices and for three patients with atrial flutter who subsequently underwent catheter mapping and radiofrequency ablation. Preliminary validation of EWI maps against invasive transcutaneous electroanatomical cardiac mapping was also demonstrated. EWI has the potential of becoming a noninvasive and highly translational technology that can serve as a unique imaging tool for the early detection, diagnosis and treatment monitoring and follow-up of arrhythmias and conduction disorders through ultrasound-based mapping of the transmural electromechanical activation sequence reliably, at the point of care, and in real time.Biomedical engineeringjp2643Biomedical EngineeringDissertationsReal-Time Noninvasive Estimation of Intrapleural Pressure in Mechanically Ventilated Patients: a Feasibility Studyhttp://academiccommons.columbia.edu/catalog/ac:171242
Albanese, Antonio; Karamolegkos, Nikolaos ; Haider, Syed W.; Seiver, Adam; Chbat, Nicolas W.http://dx.doi.org/10.7916/D8GT5K7QMon, 03 Mar 2014 00:00:00 +0000A method for real-time noninvasive estimation of intrapleural pressure in mechanically ventilated patients is proposed. The method employs a simple first-order lung mechanics model that is fitted in real-time to flow and pressure signals acquired non-invasively at the opening of the patient airways, in order to estimate lung resistance (RL), lung compliance (CL) and intrapleural pressure (Ppl) continuously in time. Estimation is achieved by minimizing the sum of squared residuals between measured and model predicted airway pressure using a modified Recursive Least Squares (RLS) approach. Particularly, two different RLS algorithms, namely the conventional RLS with Exponential Forgetting (EF-RLS) and the RLS with Vector-type Forgetting Factor (VFF-RLS), are considered in this study and their performances are first evaluated using simulated data. Simulations suggest that the conventional EFRLS algorithm is not suitable for our purposes, whereas the VFF-RLS method provides satisfactory results. The potential of the VFF-RLS based method is then proved on experimental data collected from a mechanically ventilated pig. Results show that the method provides continuous estimated lung resistance and compliance in normal physiological ranges and pleural pressure in good agreement with invasive esophageal pressure measurements.Biomedical engineering, Mechanical engineeringaa2932, nk2440, nc22Mechanical Engineering, Biomedical EngineeringConferencesProteins at Interfaces: Conformational Behavior and Wearhttp://academiccommons.columbia.edu/catalog/ac:171212
Dumont, Emmanuel Louis Pierrehttp://dx.doi.org/10.7916/D8HT2MC3Fri, 28 Feb 2014 00:00:00 +0000Proteins at interfaces play a major role in biomaterials and lab-on-a-chip devices. Protein interactions with the surface change their conformations and therefore their ability to bind to their respective ligands. Another major area of interest surrounding biomaterials and lab-on-a-chip devices is the prediction and prevention of wear. Wear is the progressive loss of material from an object caused by contact and relative movement of the contacting solid, liquid, or gas. It is estimated that wear costs 1% of the gross domestic product (approximately $150 billion for the US). With the emergence of drug-releasing implants and lab-on-the-chip devices, wear has also become a major concern in bio- and nano- technology. In our laboratory, we use microtubules (filamentous proteins) gliding on kinesin motor proteins as transporters in biosensors. This system, known as the motility assay, is ideal for studying how the conformation of kinesins impacts the gliding of microtubules and therefore the performance of the biosensor. The proposed studies seek to show that kinesins' geometry changes with their grafting density following De Gennes' scaling laws for flexible polymers (Chapter 2 , published in Langmuir as E.L.P. Dumont, H. Belmas, and H. Hess, Observing the mushroom-to-brush transition for kinesin proteins, 2013, 29 (49), 15142-15145) and that microtubules experience molecular wear due to their repeated interactions with kinesins (Chapter 3, under review for Nature Nanotechnology as E.L.P. Dumont and H. Hess, Molecular wear of microtubules propelled by surface-adhered kinesins). These two results permit the prediction of the lifetime of biosensors using kinesin-propelled microtubules (Chapter 4, to be submitted to Nano Letters as Y. Jeune-Smith, E.L.P. Dumont and H. Hess, Wear and breakage combine to mechanically degrade kinesin-powered molecular shuttles). I also discuss the importance of mechanical fatigue for molecular machine design (Chapter 5, published as H. Hess and E.L.P. Dumont, Fatigue Failure and Molecular Machine Design, Small, 7, 1619-1623, 2011). Finally, and it is unrelated to the previous chapters, I developed Monte Carlo simulations for protein adsorption on polymer-coated surfaces (Chapter 6, to be submitted as E.L.P. Dumont, A.V. Guillaume, A. Gore, and H. Hess, Random Sequential Adsorption of proteins on polymer-covered surfaces: A simulation-based approach) and I explored a molecular model to explain the fracture of materials at low stresses (Chapter 7).Biophysics, Biomedical engineeringBiomedical EngineeringDissertationsOverview of Micro- and Nano-Technology Tools for Stem Cell Applications: Micropatterned and Microelectronic Deviceshttp://academiccommons.columbia.edu/catalog/ac:171070
Cagnin, Stefano; Cimetta, Elisa; Guiducci, Carlotta; Martini, Paolo; Lanfranchi, Gerolamohttp://dx.doi.org/10.7916/D8BC3WJ0Wed, 26 Feb 2014 00:00:00 +0000In the past few decades the scientific community has been recognizing the paramount role of the cell microenvironment in determining cell behavior. In parallel, the study of human stem cells for their potential therapeutic applications has been progressing constantly. The use of advanced technologies, enabling one to mimic the in vivo stem cell microenviroment and to study stem cell physiology and physio-pathology, in settings that better predict human cell biology, is becoming the object of much research effort. In this review we will detail the most relevant and recent advances in the field of biosensors and micro- and nano-technologies in general, highlighting advantages and disadvantages. Particular attention will be devoted to those applications employing stem cells as a sensing element.Biomedical engineering, Bioinformatics, PathologyBiomedical EngineeringArticlesTransient Respiratory Response to Hypercapnia: Analysis via a Cardiopulmonary Simulation Modelhttp://academiccommons.columbia.edu/catalog/ac:171073
Albanese, Antonio; Chbat, Nicolas W.; Ursino, Maurohttp://dx.doi.org/10.7916/D86M34V3Wed, 26 Feb 2014 00:00:00 +0000In recent years, our group has developed a comprehensive cardiopulmonary (CP) model that comprises the heart, systemic and pulmonary circulations, lung mechanics and gas exchange, tissue metabolism, and cardiovascular and respiratory control mechanisms. In this paper, we analyze the response of the model to hypercapnic conditions and hence focus on the chemoreflex control mechanism. Particularly, we have enhanced the peripheral chemoreceptor model in order to better reflect respiratory control physiology. Using the CO2 fraction in the inspired air as input to the CP model, we were able to analyze the transient response of the system to CO2 step input at different levels, in terms of alveolar gas partial pressures, tidal volume, minute ventilation and respiratory frequency. Model predictions were tested against experimental data from human subjects. Results show good agreement for all the variables under study during the transient phases and low root mean square errors at steady state. This indicates the potential for the model to be used as a valid tool for clinical practice and medical research, providing a complementary way to experience-based clinical decisions.Biomedical engineering, Mechanical engineeringaa2932, nc22Mechanical Engineering, Biomedical EngineeringConferencesA Support-Based Reconstruction for SENSE MRIhttp://academiccommons.columbia.edu/catalog/ac:171058
Zhang, Yudong; Peterson, Bradley S.; Dong, Zhengchaohttp://dx.doi.org/10.7916/D8H41PG0Wed, 26 Feb 2014 00:00:00 +0000A novel, rapid algorithm to speed up and improve the reconstruction of sensitivity encoding (SENSE) MRI was proposed in this paper. The essence of the algorithm was that it iteratively solved the model of simple SENSE on a pixel-by-pixel basis in the region of support (ROS). The ROS was obtained from scout images of eight channels by morphological operations such as opening and filling. All the pixels in the FOV were paired and classified into four types, according to their spatial locations with respect to the ROS, and each with corresponding procedures of solving the inverse problem for image reconstruction. The sensitivity maps, used for the image reconstruction and covering only the ROS, were obtained by a polynomial regression model without extrapolation to keep the estimation errors small. The experiments demonstrate that the proposed method improves the reconstruction of SENSE in terms of speed and accuracy. The mean square errors (MSE) of our reconstruction is reduced by 16.05% for a 2D brain MR image and the mean MSE over the whole slices in a 3D brain MRI is reduced by 30.44% compared to those of the traditional methods. The computation time is only 25%, 45%, and 70% of the traditional method for images with numbers of pixels in the orders of 103, 104, and 105–107, respectively.Medical imaging and radiology, Neurosciences, Biomedical engineeringbp2014, zd2109PsychiatryArticlesNovel Engineering Approaches for DNA Sequencing and Analysishttp://academiccommons.columbia.edu/catalog/ac:169823
Palla, Mirkohttp://dx.doi.org/10.7916/D8K0728CMon, 03 Feb 2014 00:00:00 +0000DNA sequencing is a fundamental tool in biological and medical research. DNA molecules contain the heritable genetic information in all living organisms and encode all the proteins in our body. Therefore, determination of DNA sequence is useful in basic biological research, evolutionary biology, as well as the applied biological fields, such as diagnostic or forensic research. High-throughput DNA sequencing is essential for personalized medicine. To achieve this dream, the price of genome sequencing should be dramatically decreased to a level that most people can afford. Despite the refinements of Sanger sequencing, the current genome sequencing cost remains formidable. Therefore, revolutionary advances in DNA sequencing technology are demanded. To overcome the limitations of the current sequencing technologies, a variety of new DNA sequencing methods have been investigated with the aim of eventually realizing the goal of the $1,000 genome, including sequencing by synthesis (SBS). In this thesis, we build upon current state-of-the-art sequencing technologies such as SBS to develop novel proof-of-principle technologies for high-throughput DNA sequencing; demonstrate a general platform for high sensitivity biomolecular detection; and briefly study DNA processing protein (e.g., helicase) functions at the atomistic level. The following is a summary of the resulting work presented herein: first, a new DNA sequencing technology development is presented that utilizes surface-enhanced Raman spectroscopy (SERS); second, a novel approach of SERS-based biosensing for quantitative detection of biomolecules is demonstrated; third, a rigorous mathematical development of an analytical model is described to predict experimental SERS signal intensity distributions for biomolecular quantification; fourth, a versatile SERS-based quantitative method is developed to monitor the catalyst-free click reaction efficiency for small molecule conjugation; fifth, theoretical work using molecular dynamics simulations for analyzing the mechanical behavior of a molecular motor involved in DNA processing are described; and finally, the thesis presents a proposed nanodevice to combine the SERS-SBS technology with our bioquantification method into one functional unit. Consequently, these research efforts provide a foundation for the novel use and integration of SERS-SBS into microfluidic systems for a wide range of applications, such as high-throughput DNA sequencing and genetic diagnostics, as well as the theoretical framework to investigate DNA polymerase function at the atomic level.Chemical engineering, Biomedical engineeringmp2786Mechanical EngineeringDissertationsEngineered Microenvironments for Controlled Stem Cell Differentiationhttp://academiccommons.columbia.edu/catalog/ac:169679
Vunjak-Novakovic, Gordana; Burdick, Jason A.http://dx.doi.org/10.7916/D8542KKCFri, 31 Jan 2014 00:00:00 +0000In a developing organism, tissues emerge from coordinated sequences of cell renewal, differentiation, and assembly that are orchestrated by spatial and temporal gradients of multiple regulatory factors. The composition, architecture, signaling, and biomechanics of the cellular microenvironment act in concert to provide the necessary cues regulating cell function in the developing and adult organism. With recent major advances in stem cell biology, tissue engineering is becoming increasingly oriented toward biologically inspired in vitro cellular microenvironments designed to guide stem cell growth, differentiation, and functional assembly. The premise is that to unlock the full potential of stem cells, at least some aspects of the dynamic three-dimensional (3D) environments that are associated with their renewal, differentiation, and assembly in native tissues need to be reconstructed. In the general context of tissue engineering, we discuss the environments for guiding stem cell function by an interactive use of biomaterial scaffolds and bioreactors, and focus on the interplay between molecular and physical regulatory factors. We highlight some illustrative examples of controllable cell environments developed through the interaction of stem cell biology and tissue engineering at multiple levels.Biomedical engineeringgv2131Biomedical EngineeringArticlesOptical Mapping of Impulse Propagation in Engineered Cardiac Tissuehttp://academiccommons.columbia.edu/catalog/ac:169683
Vunjak-Novokovic, Gordana; Radisic, Milica; Fast, Vladimir G.; Sharifov, Oleg F.; Iyer, Rohin K.; Park, Hyoungshinhttp://dx.doi.org/10.7916/D81C1TVNFri, 31 Jan 2014 00:00:00 +0000Cardiac tissue engineering has a potential to provide functional, synchronously contractile tissue constructs for heart repair, and for studies of development and disease using in vivo–like yet controllable in vitro settings. In both cases, the utilization of bioreactors capable of providing biomimetic culture environments is instrumental for supporting cell differentiation and functional assembly. In the present study, neonatal rat heart cells were cultured on highly porous collagen scaffolds in bioreactors with electrical field stimulation. A hallmark of excitable tissues such as myocardium is the ability to propagate electrical impulses. We utilized the method of optical mapping to measure the electrical impulse propagation. The average conduction velocity recorded for the stimulated constructs (14.4 ± 4.1 cm/s) was significantly higher than that of the nonstimulated constructs (8.6 ± 2.3 cm/s, p = 0.003). The measured electrical propagation properties correlated to the contractile behavior and the compositions of tissue constructs. Electrical stimulation during culture significantly improved amplitude of contractions, tissue morphology, and connexin-43 expression compared to the nonsimulated controls. These data provide evidence that electrical stimulation during bioreactor cultivation can improve electrical signal propagation in engineered cardiac constructs.Biomedical engineeringgv2131Biomedical EngineeringArticlesVascular Endothelial Growth Factor Secretion by Nonmyocytes Modulates Connexin-43 Levels in Cardiac Organoidshttp://academiccommons.columbia.edu/catalog/ac:169689
Vunjak-Novakovic, Gordana; Iyer, Rohin K.; Odedra, Devang; Chiu, Loraine L.Y.; Radisic, Milicahttp://dx.doi.org/10.7916/D8RV0KPGFri, 31 Jan 2014 00:00:00 +0000We previously showed that the sequential, but not simultaneous, culture of endothelial cells (ECs), fibroblasts (FBs), and cardiomyocytes (CMs) resulted in elongated, beating cardiac organoids. We hypothesized that the expression of Cx43 and contractile function are mediated by vascular endothelial growth factor (VEGF) released by nonmyocytes during the preculture period. Cardiac organoids (200 μm diameter) were cultivated in microchannels to enable rapid screening. Three experimental groups were formed: (i) Simultaneous Preculture (ECs+FBs for 48 h, followed by CMs), (ii) Sequential Preculture (ECs for 24 h, FBs for 24 h, followed by CMs), and (iii) Simultaneous Triculture (ECs+FBs+CMs). Controls included CMs only, FBs only, and ECs only groups, and preculture with ECs only or FBs only. The highest VEGF levels were found in the Preculture groups [Simultaneous Preculture, 8.9 plus or minus 2.7 ng/(mL times h−1); Sequential Preculture, 16.6 plus or minus 3.4 ng/(mL times h−1)], as compared with Simultaneous Triculture where VEGF was not detectable, as shown by enzyme-linked immunosorbent assay. Analytical flow cytometry showed that VEGFR2 was expressed by ECs (86% plus or minus 2 VEGFR2+), FBs (44% plus or minus 1 VEGFR2+), and CMs (49% plus or minus 2 VEGFR2+), showing that all three cell types were capable of responding to changes in VEGF. Addition of anti-VEGF neutralizing IgG (0.4 μg/mL) to Simultaneous Preculture resulted in 3-fold decrease in Cx43 mRNA and 1.5-fold decrease in Cx43 protein, while Simultaneous Triculture supplemented with VEGF ligand (30 ng/mL) had a threefold increase in Cx43 mRNA and a twofold increase in Cx43 protein. Addition of a small molecule inhibitor of the VEGFR2 receptor (19.4 nM) to Sequential Preculture caused a 1.4-fold decrease in Cx43 mRNA and a 4.1-fold decrease in Cx43 protein. Cx43 was localized within CMs, and not within FBs or ECs. Enriched CM organoids and Sequential Preculture organoids grown in the presence of VEGFR2 inhibitor displayed low levels of Cx43 and poor functional properties. Taken together, these results suggest that endogenous VEGF-VEGFR2 signaling enhanced Cx43 expression and cardiac function in engineered cardiac organoids.Biomedical engineeringgv2131Biomedical EngineeringArticlesLipolytic Function of Adipocyte/Endothelial Cocultureshttp://academiccommons.columbia.edu/catalog/ac:169686
Vunjak-Novakovic, Gordana; Choi, Jennifer H.; Bellas, Evangelia; Gimble, Jeffrey M.; Kaplan, David L.http://dx.doi.org/10.7916/D8WM1BCRFri, 31 Jan 2014 00:00:00 +0000The rising incidence of adipose-related disorders such as obesity has prompted increased interest in the in vitro development of functional human soft tissues to study the disease and treatment options. Further, soft tissues maintained in vitro with a capacity to resemble in vivo tissues in structure and metabolic function would help gain insight into mechanisms involved in adipose tissue development. In the current study, the metabolic potential of adipose/endothelial cocultures on three-dimensional silk fibroin scaffolds was studied. Endothelial contributions to adipose lipogenesis and lipolysis were the focus of the study. Triglyceride accumulation, adipogenic gene transcript expression, and basal lipolysis measurements demonstrated the ability of this coculture system to retain metabolic levels obtained in adipocyte monocultures. Additionally, basal lipolysis was stimulated in mono- and coculture systems to a similar extent at 1.6- and 1.9-fold over controls, respectively. The ability to maintain adipose functions in these cocultures represents a step forward in the development of a tissue-engineered adipose tissue system exhibiting both endothelial lumens and metabolic functions.Biomedical engineeringgv2131Biomedical EngineeringArticlesIn Vitro Model of Vascularized Bone: Synergizing Vascular Development and Osteogenesishttp://academiccommons.columbia.edu/catalog/ac:169760
Correia, Cristina; Vunjak-Novakovic, Gordana; Grayson, Warren L.; Park, Miri; Hutton, Daphne; Zhou, Bin; Guo, Xiang-Dong Edward; Niklason, Laura; Sousa, Rui A.; Reis, Rui L.http://dx.doi.org/10.7916/D8SQ8XD0Fri, 31 Jan 2014 00:00:00 +0000Tissue engineering provides unique opportunities for regenerating diseased or damaged tissues using cells obtained from tissue biopsies. Tissue engineered grafts can also be used as high fidelity models to probe cellular and molecular interactions underlying developmental processes. In this study, we co-cultured human umbilical vein endothelial cells (HUVECs) and human mesenchymal stem cells (MSCs) under various environmental conditions to elicit synergistic interactions leading to the colocalized development of capillary-like and bone-like tissues. Cells were encapsulated at the 1:1 ratio in fibrin gel to screen compositions of endothelial growth medium (EGM) and osteogenic medium (OM). It was determined that, to form both tissues, co-cultures should first be supplied with EGM followed by a 1:1 cocktail of the two media types containing bone morphogenetic protein-2. Subsequent studies of HUVECs and MSCs cultured in decellularized, trabecular bone scaffolds for 6 weeks assessed the effects on tissue construct of both temporal variations in growth-factor availability and addition of fresh cells. The resulting grafts were implanted subcutaneously into nude mice to determine the phenotype stability and functionality of engineered vessels. Two important findings resulted from these studies: (i) vascular development needs to be induced prior to osteogenesis, and (ii) the addition of additional hMSCs at the osteogenic induction stage improves both tissue outcomes, as shown by increased bone volume fraction, osteoid deposition, close proximity of bone proteins to vascular networks, and anastomosis of vascular networks with the host vasculature. Interestingly, these observations compare well with what has been described for native development. We propose that our cultivation system can mimic various aspects of endothelial cell – osteogenic precursor interactions in vivo, and could find utility as a model for studies of heterotypic cellular interactions that couple blood vessel formation with osteogenesis.Biomedical engineeringgv2131, bz2159, exg1Biomedical EngineeringArticlesSequential Application of Steady and Pulsatile Medium Perfusion Enhanced the Formation of Engineered Bonehttp://academiccommons.columbia.edu/catalog/ac:169692
Vunjak-Novakovic, Gordana; Correia, Cristina; Bhumiratana, Sarindr; Sousa, Rui A.; Reis, Rui L.http://dx.doi.org/10.7916/D8N58JBSFri, 31 Jan 2014 00:00:00 +0000In native bone, cells experience fluctuating shear forces that are induced by pulsatile interstitial flow associated with habitual loading. We hypothesized that the formation of engineered bone can be augmented by replicating such physiologic stimuli to osteogenic cells cultured in porous scaffolds using bioreactors with medium perfusion. To test this hypothesis, we investigated the effect of fluid flow regime on in vitro bone-like tissue development by human adipose stem cells (hASC) cultivated on porous three-dimensional silk fibroin scaffolds. To this end, we varied the sequential relative durations of steady flow (SF) and pulsatile flow (PF) of culture medium applied over a period of 5 weeks, and evaluated their effect on early stages of bone formation. Porous silk fibroin scaffolds (400-600 μm pore size) were seeded with hASC (30×106 cells/mL) and cultured in osteogenic medium under four distinct fluid flow regimes: (1) PF for 5 weeks; (2) SF for 1 week, PF for 4 weeks; (3) SF for 2 weeks, PF for 3 weeks; (4) SF for 5 weeks. The PF was applied in 12 h intervals, with the interstitial velocity fluctuating between 400 and 1200 μm/s at a 0.5 Hz frequency for 2 h, followed by 10 h of SF. In all groups, SF was applied at 400 μm/s. The best osteogenic outcomes were achieved for the sequence of 2 weeks of SF and 3 weeks of PF, as evidenced by gene expression (including the PGE2 mechanotransduction marker), construct compositions, histomorphologies, and biomechanical properties. We thus propose that osteogenesis in hASC and the subsequent early stage bone development involve a mechanism, which detects and responds to the level and duration of hydrodynamic shear forces.Biomedical engineeringgv2131Biomedical EngineeringArticlesInsulin, Ascorbate, and Glucose Have a Much Greater Influence Than Transferrin and Selenous Acid on the In Vitro Growth of Engineered Cartilage in Chondrogenic Mediahttp://academiccommons.columbia.edu/catalog/ac:169698
Vunjak-Novakovic, Gordana; Cigan, Alexander D.; Nims, Robert J.; Albro, Michael B.; Esau, John D.; Dreyer, Marissa P.; Hung, Clark T.; Ateshian, Gerard A.http://dx.doi.org/10.7916/D8HD7SNHFri, 31 Jan 2014 00:00:00 +0000The primary goal of this study was to characterize the response of chondrocyte-seeded agarose constructs to varying concentrations of several key nutrients in a chondrogenic medium, within the overall context of optimizing the key nutrients and the placement of nutrient channels for successful growth of cartilage tissue constructs large enough to be clinically relevant in the treatment of osteoarthritis (OA). To this end, chondrocyte-agarose constructs (phi4x2.34 mm, 30x106 cells/mL) were subjected to varying supplementation levels of insulin (0× to 30× relative to standard supplementation), transferrin (0x to 30x), selenous acid (0x to 10x), ascorbate (0x to 30x), and glucose (0x to 3x). The quality of resulting engineered tissue constructs was evaluated by their compressive modulus (E-Y), tensile modulus (E+Y), hydraulic permeability (k), and content of sulfated glycosaminoglycans (sGAG) and collagen (COL); DNA content was also quantified. Three control groups from two separate castings of constructs (1x concentrations of all medium constituents) were used. After 42 days of culture, values in each of these controls were, respectively, E-Y=518 plus or minus 78, 401 plus or minus 113, 236 plus or minus 67 kPa; E+Y=1420 plus or minus 430, 1140 plus or minus 490, 1240 plus or minus 280 kPa; k=2.3 plus or minus 0.8x10-3, 5.4 plus or minus 7.0x10-3, 3.3 plus or minus 1.3x10-3 mm4/N times s; sGAG=7.8 plus or minus 0.3, 6.3 plus or minus 0.4, 4.1 plus or minus 0.5%/ww; COL=1.3 plus or minus 0.2, 1.1 plus or minus 0.3, 1.4 plus or minus 0.4%/ww; and DNA=11.5 plus or minus 2.2, 12.1 plus or minus 0.6, 5.2 plus or minus 2.8 μg/disk. The presence of insulin and ascorbate was essential, but their concentrations may drop as low as 0.3x without detrimental effects on any of the measured properties; excessive supplementation of ascorbate (up to 30x) was detrimental to E-Y, and 30x insulin was detrimental to both E+Y and E-Y. The presence of glucose was similarly essential, and matrix elaboration was significantly dependent on its concentration (p less than 10-6), with loss of functional properties, composition, and cellularity observed at less than or equal to 0.3x; excessive glucose supplementation (up to 3x) showed no detrimental effects. In contrast, transferrin and selenous acid had no influence on matrix elaboration. These findings suggest that adequate distributions of insulin, ascorbate, and glucose, but not necessarily of transferrin and selenous acid, must be ensured within large engineered cartilage constructs to produce a viable substitute for joint tissue lost due to OA.Biomedical engineeringgv2131Biomedical EngineeringArticlesMicro-Bioreactor Array for Controlling Cellular Microenvironmentshttp://academiccommons.columbia.edu/catalog/ac:169724
Vunjak-Novakovic, Gordana; Figallo, Elisa; Cannizzaro, Christopher; Gerecht, Sharon; Burdick, Jason A.; Langer, Robert; Elvassore, Nicolahttp://dx.doi.org/10.7916/D8GF0RG7Fri, 31 Jan 2014 00:00:00 +0000High throughput experiments can be used to spatially and temporally investigate the many factors that regulate cell differentiation. We have developed a micro-bioreactor array (MBA) that is fabricated using soft lithography and contains twelve independent micro-bioreactors perfused with culture medium. The MBA enables cultivation of cells that are either attached to substrates or encapsulated in hydrogels, at variable levels of hydrodynamic shear, and with automated image analysis of the expression of cell differentiation markers. The flow and mass transport in the MBA were characterized by computational fluid dynamic (CFD) modeling. The representative MBA configurations were validated using the C2C12 cell line, primary rat cardiac myocytes and human embryonic stem cells (hESCs) (lines H09 and H13). To illustrate the utility of the MBA for controlled studies of hESCs, we established correlations between the expression of smooth muscle actin and cell density for three different flow configurations.Biomedical engineeringgv2131Biomedical EngineeringArticlesCardiac Tissue Engineeringhttp://academiccommons.columbia.edu/catalog/ac:169712
Vunjak-Novakovic, Gordana; Radisic, Milicahttp://dx.doi.org/10.7916/D8CN71WQFri, 31 Jan 2014 00:00:00 +0000We hypothesized that clinically sized (1-5 mm thick),compact cardiac constructs containing physiologically high density of viable cells (~108 cells/cm3) can be engineered in vitro by using biomimetic culture systems capable of providing oxygen transport and electrical stimulation, designed to mimic those in native heart. This hypothesis was tested by culturing rat heart cells on polymer scaffolds, either with perfusion of culture medium (physiologic interstitial velocity, supplementation of perfluorocarbons), or with electrical stimulation (continuous application of biphasic pulses, 2 ms, 5 V, 1 Hz). Tissue constructs cultured without perfusion or electrical stimulation served as controls. Medium perfusion and addition of perfluorocarbons resulted in compact, thick constructs containing physiologic density of viable, electromechanically coupled cells, in contrast to control constructs which had only a ~100 mm thick peripheral region with functionally connected cells. Electrical stimulation of cultured constructs resulted in markedly improved contractile properties, increased amounts of cardiac proteins, and remarkably well developed ultrastructure (similar to that of native heart) as compared to non-stimulated controls. We discuss here the state of the art of cardiac tissue engineering, in light of the biomimetic approach that reproduces in vitro some of the conditions present during normal tissue development.Biomedical engineeringgv2131Biomedical EngineeringArticlesDerivation of Two New Human Embryonic Stem Cell Lines from Nonviable Human Embryoshttp://academiccommons.columbia.edu/catalog/ac:169757
Gavrilov, Svetlana; Vunjak-Novakovic, Gordana; Marolt, Darja; Douglas, Nataki C.; Prosser, Robert W.; Khalid, Imran; Sauer, Mark V.; Landry, Donald W.; Papaioannou, Virginia E.http://dx.doi.org/10.7916/D82805K3Fri, 31 Jan 2014 00:00:00 +0000We report the derivation and characterization of two new human embryonic stem cells (hESC) lines (CU1 and CU2) from embryos with an irreversible loss of integrated organismic function. In addition, we analyzed retrospective data of morphological progression from embryonic day (ED) 5 to ED6 for 2480 embryos not suitable for clinical use to assess grading criteria indicative of loss of viability on ED5. Our analysis indicated that a large proportion of in vitro fertilization (IVF) embryos not suitable for clinical use could be used for hESC derivation. Based on these combined findings, we propose that criteria commonly used in IVF clinics to determine optimal embryos for uterine transfer can be employed to predict the potential for hESC derivation from poor quality embryos without the destruction of vital human embryos.Biomedical engineeringgv2131, dm2453, nd2058, rwp3, mvs9, dwl1, vep1Obstetrics and Gynecology, Medicine, Genetics and Development, Biomedical EngineeringArticlesGeometric Control of Human Stem Cell Morphology and Differentiationhttp://academiccommons.columbia.edu/catalog/ac:169751
Vunjak-Novakovic, Gordana; Wan, Leo Q.; Kang, Sylvia M.; Eng, George; Grayson, Warren L.; Lu, Xin; Huo, Bo; Gimble, Jeffrey; Guo, Xiang-Dong Edward; Mow, Van C.http://dx.doi.org/10.7916/D89P2ZM4Fri, 31 Jan 2014 00:00:00 +0000During tissue morphogenesis, stem cells and progenitor cells migrate, proliferate, and differentiate, with striking changes in cell shape, size, and acting mechanical stresses. The local cellular function depends on the spatial distribution of cytokines as well as local mechanical microenvironments in which the cells reside. In this study, we controlled the organization of human adipose derived stem cells using micro-patterning technologies, to investigate the influence of multi-cellular form on spatial distribution of cellular function at an early stage of cell differentiation. The underlying role of cytoskeletal tension was probed through drug treatment. Our results show that the cultivation of stem cells on geometric patterns resulted in pattern- and position-specific cell morphology, proliferation and differentiation. The highest cell proliferation occurred in the regions with large, spreading cells (such as the outer edge of a ring and the short edges of rectangles). In contrast, stem cell differentiation co-localized with the regions containing small, elongated cells (such as the inner edge of a ring and the regions next to the short edges of rectangles). The application of drugs that inhibit the formation of actomyosin resulted in the lack of geometrically specific differentiation patterns. This study confirms the role of substrate geometry on stem cell differentiation, through associated physical forces, and provides a simple and controllable system for studying biophysical regulation of cell function.Biomedical engineeringgv2131, gme2103, xl2402, exg1, vcm1Computer Science, Medicine, Biomedical EngineeringArticlesSurface-Patterned Electrode Bioreactor for Electrical Stimulationhttp://academiccommons.columbia.edu/catalog/ac:169733
Vunjak-Novakovic, Gordana; Tandon, Nina; Marsano, Anna; Maidhof, Robert; Numata, Keiji; Montouri-Sorrentino, Chrystina; Cannizzaro, Christopher; Voldman, Joelhttp://dx.doi.org/10.7916/D8348HB2Fri, 31 Jan 2014 00:00:00 +0000We present a microscale cell culture system with an interdigitated microarray of excimer-laser-ablated indium tin oxide electrodes for electrical stimulation of cultured cells. The system has been characterized in a range of geometeries and stimulation regimes via electrochemical impedance spectroscopy and used to culture primary cardiomyocytes and human adipose derived stem cells. Over 6 days of culture with electrical stimulation (2 ms duration, 1 Hz, 180 μm wide electrodes with 200 μm spacing), both cell types exhibited enhanced proliferation, elongation and alignment, and adipose derived stem cells exhibited higher numbers of Connexin-43-composed gap junctions.Biomedical engineeringgv2131, nmt2104Pharmacology, Biomedical EngineeringArticlesMicrofluidic Bioreactor for Dynamic Regulation of Early Mesodermal Commitment in Human Pluripotent Stem Cellshttp://academiccommons.columbia.edu/catalog/ac:169742
Vunjak-Novakovic, Gordana; Cimetta, Elisa; Sirabella, Dario; Yeager, Keith; Davidson, Kathryn; Simon, Joseph; Moon, Randall T.http://dx.doi.org/10.7916/D8K64G2KFri, 31 Jan 2014 00:00:00 +0000During development and regeneration, tissues emerge from coordinated sequences of stem cell renewal, specialization and assembly that are orchestrated by cascades of regulatory signals. The complex and dynamic in vivo milieu cannot be replicated using standard in vitro techniques. Microscale technologies now offer potential for conducting highly controllable and sophisticated experiments at biologically relevant scales, with real-time insights into cellular responses. We developed a microbioreactor providing time sequences of space-resolved gradients of multiple molecular factors in three-dimensional (3D) cell culture settings, along with a versatile, high-throughput operation and imaging compatibility. A single microbioreactor yields up to 120 data points, corresponding to 15 replicates of a gradient with 8 concentration levels. Embryoid bodies (EBs) obtained from human embryonic and induced pluripotent stem cells (hESC, hiPSC) were exposed to concentration gradients of Wnt3a, Activin A, BMP4 and their inhibitors, to get new insights into the early-stage fate specification and mesodermal lineage commitment. We were able to evaluate the initiation of mesodermal induction by measuring and correlating the gene expression profiles to the concentration gradients of mesoderm-inducing morphogens. We propose that the microbioreactor systems combining spatial and temporal gradients of molecular and physical factors to hESC and hiPSC cultures can form a basis for predictable in vitro models of development and disease.Biomedical engineeringgv2131, ec2438, ds3116, ky2161Biomedical EngineeringArticlesMicrofluidic Device Generating Stable Concentration Gradients for Long-Term Cell Culture: Application to Wnt3a Regulation of B-catenin signalinghttp://academiccommons.columbia.edu/catalog/ac:169739
Vunjak-Novokovic, Gordana; Cimetta, Elisa; Cannizzaro, Christopher; James, Richard; Biechele, Travis; Moon, Randall T.; Elvassore, Nicolahttp://dx.doi.org/10.7916/D8ZC80VRFri, 31 Jan 2014 00:00:00 +0000In developing tissues, proteins and signaling molecules present themselves in the form of concentration gradients, which determine the fate specification and behavior of the sensing cells. To mimic these conditions in vitro, we developed a microfluidic device designed to generate stable concentration gradients at low hydrodynamic shear and allowing long term culture of adhering cells. The gradient forms in a culture space between two parallel laminar flow streams of culture medium at two different concentrations of a given morphogen. The exact algorithm for defining the concentration gradients was established with the aid of mathematical modeling of flow and mass transport. Wnt3a regulation of B-catenin signaling was chosen as a case study. The highly conserved Wnt-activated B-catenin pathway plays major roles in embryonic development, stem cell proliferation and differentiation. Wnt3a stimulates the activity of B-catenin pathway, leading to translocation of B-catenin to the nucleus where it activates a series of target genes. We cultured A375 cells stably expressing a Wnt/B-catenin reporter driving the expression of Venus, pBARVS, inside the microfluidic device. The extent to which the B-catenin pathway was activated in response to a gradient of Wnt3a was assessed in real time using the BARVS reporter gene. On a single cell level, the B-catenin signaling was proportionate to the concentration gradient of Wnt3a; we thus propose that the modulation of Wnt3a gradients in real time can provide new insights into the dynamics of B-catenin pathway, under conditions that replicate some aspects of the actual cell-tissue milieu. Our device thus offers a highly controllable platform for exploring the effects of concentration gradients on cultured cells.Biomedical engineeringgv2131, ec2438Biomedical EngineeringArticlesPatterning Osteogenesis by Inducible Gene Expression in Microfluidic Culture Systemshttp://academiccommons.columbia.edu/catalog/ac:169754
Vunjak-Novakovic, Gordana; Zhang, Yue; Gazit, Zulma; Pelled, Gadi; Gazit, Danhttp://dx.doi.org/10.7916/D85X26X7Fri, 31 Jan 2014 00:00:00 +0000The development of transitional interfacial zones between adjacent tissues remains a significant challenge for developing tissue engineering and regenerative medicine strategies. Using osteogenic differentiation as a model, we describe a novel approach to spatially regulate expression and secretion of the bone morphogenetic protein (BMP-2) in a two-dimensional field of cultured cells, by flow patterning the modulators of inducible BMP-2 gene expression. We first demonstrate control of gene expression, and of osteogenic differentiation of the cell line with inducible expression of BMP-2. Then we design laminar flow systems, with patterned delivery of Doxycycline (Dox), the expression modulator of BMP-2. The patterned concentration profiles were verified by computational simulation and dye separation experiments. Patterned differentiation experiments conducted in the flow systems for a period of three weeks showed the Dox concentration dependent osteogenic differentiation, as evidenced by mineral deposition. In summary, by combining inducible gene expression with laminar flow technologies, this study provided an innovative way to engineer tissue interfaces.Biomedical engineeringgv2131Biomedical EngineeringArticlesEngineered Microenvironments for Controlled Stem Cell Differentiationhttp://academiccommons.columbia.edu/catalog/ac:169058
Burdick, Jason A.; Vunjak-Novakovic, Gordanahttp://dx.doi.org/10.7916/D8MG7MGTThu, 23 Jan 2014 00:00:00 +0000In a developing organism, tissues emerge from coordinated sequences of cell renewal, differentiation, and assembly that are orchestrated by spatial and temporal gradients of multiple regulatory factors. The composition, architecture, signaling, and biomechanics of the cellular microenvironment act in concert to provide the necessary cues regulating cell function in the developing and adult organism. With recent major advances in stem cell biology, tissue engineering is becoming increasingly oriented toward biologically inspired in vitro cellular microenvironments designed to guide stem cell growth, differentiation, and functional assembly. The premise is that to unlock the full potential of stem cells, at least some aspects of the dynamic three-dimensional (3D) environments that are associated with their renewal, differentiation, and assembly in native tissues need to be reconstructed. In the general context of tissue engineering, we discuss the environments for guiding stem cell function by an interactive use of biomaterial scaffolds and bioreactors, and focus on the interplay between molecular and physical regulatory factors. We highlight some illustrative examples of controllable cell environments developed through the interaction of stem cell biology and tissue engineering at multiple levels.Biomedical engineeringgv2131Biomedical EngineeringArticlesOptical Mapping of Impulse Propagation in Engineered Cardiac Tissuehttp://academiccommons.columbia.edu/catalog/ac:169048
Radisic, Milica; Vunjak-Novakovic, Gordana; Fast, Vladimir G.; Sharifov, Oleg F.; Iyer, Rohin K.; Park, Hyoungshinhttp://dx.doi.org/10.7916/D8R78C53Thu, 23 Jan 2014 00:00:00 +0000Cardiac tissue engineering has a potential to provide functional, synchronously contractile tissue constructs for heart repair, and for studies of development and disease using in vivo-like yet controllable in vitro settings. In both cases, the utilization of bioreactors capable of providing biomimetic culture environments is instrumental for supporting cell differentiation and functional assembly. In the present study, neonatal rat heart cells were cultured on highly porous collagen scaffolds in bioreactors with electrical field stimulation. A hallmark of excitable tissues such as myocardium is the ability to propagate electrical impulses. We utilized the method of optical mapping to measure the electrical impulse propagation. The average conduction velocity recorded for the stimulated constructs (14.4 plus or minus 4.1 cm/s) was significantly higher than that of the nonstimulated constructs (8.6 plus or minus 2.3 cm/s, p = 0.003). The measured electrical propagation properties correlated to the contractile behavior and the compositions of tissue constructs. Electrical stimulation during culture significantly improved amplitude of contractions, tissue morphology, and connexin-43 expression compared to the nonsimulated controls. These data provide evidence that electrical stimulation during bioreactor cultivation can improve electrical signal propagation in engineered cardiac constructs.Biomedical engineeringgv2131Biomedical EngineeringArticlesGene Transfer of a Human Insulin-Like Growth Factor I cDNA Enhances Tissue Engineering of Cartilagehttp://academiccommons.columbia.edu/catalog/ac:169018
Madry, Henning; Vunjak-Novakovic, Gordana; Padera, Robert; Seidel, Joachim; Langer, Robert; Freed, Lisa E.; Trippel, Stephen B.http://dx.doi.org/10.7916/D8VX0DHSThu, 23 Jan 2014 00:00:00 +0000The repair of articular cartilage lesions remains a clinical problem. Two novel approaches to cartilage formation, gene transfer and tissue engineering, have been limited by short-term transgene expression in transplanted chondrocytes and inability to deliver regulatory signals to engineered tissues according to specific temporal and spatial patterns. We tested the hypothesis that the transfer of a cDNA encoding the human insulin-like growth factor I (IGF-I) can provide sustained gene expression in cell-polymer constructs in vitro and in vivo and enhance the structural and functional properties of tissue-engineered cartilage. Bovine articular chondrocytes genetically modified to overexpress human IGF-I were seeded into polymer scaffolds, cultured in bioreactors in serum-free medium, and implanted subcutaneously in nude mice; constructs based on nontransfected or lacZ-transfected chondrocytes served as controls. Transgene expression was maintained throughout the duration of the study, more than 4 weeks in vitro followed by an additional 10 days either in vitro or in vivo. Chondrogenesis progressed toward the formation of cartilaginous tissue that was characterized by the presence of glycosaminoglycans, aggrecan, and type II collagen, and the absence of type I collagen. IGF-I constructs contained increased amounts of glycosaminoglycans and collagen and confined-compression equilibrium moduli as compared with controls; all groups had subnormal cellularity. The amounts of glycosaminoglycans and collagen per unit DNA in IGF-I constructs were markedly higher than in constructs cultured in serum-supplemented medium or native cartilage. This enhancement of chondrogenesis by spatially defined overexpression of human IGF-I suggests that cartilage tissue engineering based on genetically modified chondrocytes may be advantageous as compared with either gene transfer or tissue engineering alone.Biomedical engineeringgv2131Biomedical EngineeringArticlesBiofabrication Enables Efficient Interrogation and Optimization of Sequential Culture of Endothelial Cells, Fibroblasts, and Cardiomyocytes for Formation of Vascular Cords in Cardiac Tissue Engineeringhttp://academiccommons.columbia.edu/catalog/ac:169009
Iyer, Rohin K.; Vunjak-Novakovic, Gordana; Chiu, Loraine L. Y.; Radisic, Milicahttp://dx.doi.org/10.7916/D80P0X03Thu, 23 Jan 2014 00:00:00 +0000Biofabrication of living structures with desired topology and functionality requires the interdisciplinary effort of practitioners of the physical, life and engineering sciences. Such efforts are being undertaken in many laboratories around the world. Numerous approaches are pursued, such as those based on the use of natural or artificial scaffolds, decellularized cadaveric extracellular matrices and, most lately, bioprinting. To be successful in this endeavor, it is crucial to provide in vitro micro-environmental clues for the cells resembling those in the organism. Therefore, scaffolds, populated with differentiated cells or stem cells, of increasing complexity and sophistication are being fabricated. However, no matter how sophisticated scaffolds are, they can cause problems stemming from their degradation, eliciting immunogenic reactions and other a priori unforeseen complications. It is also being realized that ultimately the best approach might be to rely on the self-assembly and self-organizing properties of cells and tissues and the innate regenerative capability of the organism itself, not just simply prepare tissue and organ structures in vitro followed by their implantation. Here we briefly review the different strategies for the fabrication of three-dimensional biological structures, in particular bioprinting. We detail a fully biological, scaffoldless, print-based engineering approach that uses self-assembling multicellular units as bio-ink particles and employs early developmental morphogenetic principles, such as cell sorting and tissue fusion.Biomedical engineeringgv2131Biomedical EngineeringArticlesControllable Expansion of Primary Cardiomyocytes by Reversible Immortalizationhttp://academiccommons.columbia.edu/catalog/ac:169061
Vunjak-Novakovic, Gordana; Zhang, Yue; Nuglozeh, Edem; Touré, Fatouma; Schmidt, Ann Mariehttp://dx.doi.org/10.7916/D8GQ6VQNThu, 23 Jan 2014 00:00:00 +0000Cardiac tissue engineering will remain only a prospect unless large numbers of therapeutic cells can be provided, either from small samples of cardiac cells or from stem cell sources. In contrast to most adult cells, cardiomyocytes are terminally differentiated and cannot be expanded in culture. We explored the feasibility of enabling the in vitro expansion of primary neonatal rat cardiomyocytes by lentivector-mediated cell immortalization, and then reverting the phenotype of the expanded cells back to the cardiomyocyte state. Primary rat cardiomyocytes were transduced with simian virus 40 large T antigen (TAg), or with Bmi-1 followed by the human telomerase reverse transcriptase (hTERT) gene; the cells were expanded; and the transduced genes were removed by adenoviral vector expressing Cre recombinase. The TAg gene was more efficient in cell transduction than the Bmi-1/hTERT gene, based on the rate of cell proliferation. Immortalized cells exhibited the morphological features of dedifferentiation (increased vimentin expression, and reduced expression of troponin I and Nkx2.5) along with the continued expression of cardiac markers (α-actin, connexin-43, and calcium transients). After the immortalization was reversed, cells returned to their differentiated state. This strategy for controlled expansion of primary cardiomyocytes by gene transfer has potential for providing large amounts of a patient's own cardiomyocytes for cell therapy, and the cardiomyocytes derived by this method could be a useful cellular model by which to study cardiogenesis.Biomedical engineeringgv2131Biomedical EngineeringArticlesMicropatterning of Cells Reveals Chiral Morphogenesishttp://academiccommons.columbia.edu/catalog/ac:168991
Vunjak-Novakovic, Gordana; Wan, Leo Q.; Ronaldson, Kacey; Guirguis, Markhttp://dx.doi.org/10.7916/D8WW7FM5Thu, 23 Jan 2014 00:00:00 +0000Invariant left-right (LR) patterning or chirality is critical for embryonic development. The loss or reversal of LR asymmetry is often associated with malformations and disease. Although several theories have been proposed, the exact mechanism of the initiation of the LR symmetry has not yet been fully elucidated. Recently, chirality has been detected within single cells as well as multicellular structures using several in vitro approaches. These studies demonstrated the universality of cell chirality, its dependence on cell phenotype, and the role of physical boundaries. In this review, we discuss the theories for developmental LR asymmetry, compare various in vitro cell chirality model systems, and highlight possible roles of cell chirality in stem cell differentiation. We emphasize that the in vitro cell chirality systems have great promise for helping unveil the nature of chiral morphogenesis in development.Biomedical engineeringgv2131, kr2411Biomedical EngineeringArticlesTissue Engineering by Self-Assembly and Bioprinting of Living Cellshttp://academiccommons.columbia.edu/catalog/ac:169006
Jakab, Karoly; Vunjak-Novakovic, Gordana; Norotte, Cyrille; Marga, Francoise; Murphy, Keith; Forgacs, Gaborhttp://dx.doi.org/10.7916/D84F1NPZThu, 23 Jan 2014 00:00:00 +0000Biofabrication of living structures with desired topology and functionality requires the interdisciplinary effort of practitioners of the physical, life and engineering sciences. Such efforts are being undertaken in many laboratories around the world. Numerous approaches are pursued, such as those based on the use of natural or artificial scaffolds, decellularized cadaveric extracellular matrices and, most lately, bioprinting. To be successful in this endeavor, it is crucial to provide in vitro micro-environmental clues for the cells resembling those in the organism. Therefore, scaffolds, populated with differentiated cells or stem cells, of increasing complexity and sophistication are being fabricated. However, no matter how sophisticated scaffolds are, they can cause problems stemming from their degradation, eliciting immunogenic reactions and other a priori unforeseen complications. It is also being realized that ultimately the best approach might be to rely on the self-assembly and self-organizing properties of cells and tissues and the innate regenerative capability of the organism itself, not just simply prepare tissue and organ structures in vitro followed by their implantation. Here we briefly review the different strategies for the fabrication of three-dimensional biological structures, in particular bioprinting. We detail a fully biological, scaffoldless, print-based engineering approach that uses self-assembling multicellular units as bio-ink particles and employs early developmental morphogenetic principles, such as cell sorting and tissue fusion.Biomedical engineeringgv2131Biomedical EngineeringArticlesAutologous Cell Therapies for Bone Tissue Regenerationhttp://academiccommons.columbia.edu/catalog/ac:168994
Rode, Matjaz; Krkovic, Matija; Senekovic, Vladimir; Vunjak-Novakovic, Gordana; Knezevic, Miomir; Frohlich, Mirjam; Gantar, Danica; Malicev, Elvira; Krecic-Stres, Hana; Kregar-Velikonja, Nevenkahttp://dx.doi.org/10.7916/D8NG4NKRThu, 23 Jan 2014 00:00:00 +0000The healing potential of bone is sufficient to restore simple fractures, which are generally treated by standard conservative or surgical therapy. However, in some cases, reparative osteogenesis does not result in structural and functional recovery of the bone. Extended bone defects following trauma or cancer resection or non-unions of fractures may require more sophisticated treatment. In these cases, bone grafting procedures, segmental bone transport, distraction osteogenesis or biomaterials are applied for reconstruction.Biomedical engineeringgv2131Biomedical EngineeringBook chaptersVascular Progenitor Cells Isolated from Human Embryonic Stem Cellshttp://academiccommons.columbia.edu/catalog/ac:168997
Vunjak-Novakovic, Gordana; Ferreira, Lino S.; Gerecht, Sharon; Shieh, Hester F.; Watson, Nicki; Rupnick, Maria A.; Dallabrida, Susan M.; Langer, Roberthttp://dx.doi.org/10.7916/D8HQ3WWGThu, 23 Jan 2014 00:00:00 +0000Invariant left-right (LR) patterning or chirality is critical for embryonic development. The loss or reversal of LR asymmetry is often associated with malformations and disease. Although several theories have been proposed, the exact mechanism of the initiation of the LR symmetry has not yet been fully elucidated. Recently, chirality has been detected within single cells as well as multicellular structures using several in vitro approaches. These studies demonstrated the universality of cell chirality, its dependence on cell phenotype, and the role of physical boundaries. In this review, we discuss the theories for developmental LR asymmetry, compare various in vitro cell chirality model systems, and highlight possible roles of cell chirality in stem cell differentiation. We emphasize that the in vitro cell chirality systems have great promise for helping unveil the nature of chiral morphogenesis in development.Biomedical engineeringgv2131Biomedical EngineeringArticlesPhotocrosslinked Biodegradable Fibrous Scaffolds with Tunable Properties for Tissue Engineering Applicationshttp://academiccommons.columbia.edu/catalog/ac:169003
Burdick, Jason A.; Vunjak-Novakovic, Gordana; Ifkovits, Jamie L.; Devlin, Jeffrey J.; Eng, George; Martens, Timothy P.http://dx.doi.org/10.7916/D8862DDPThu, 23 Jan 2014 00:00:00 +0000It is becoming increasingly apparent that the architecture and mechanical properties of scaffolds, particularly with respect to mimicking features of natural tissues, are important for tissue engineering applications. Acrylated poly(glycerol sebacate) (Acr-PGS) is a material that can be crosslinked upon exposure to ultraviolet light, leading to networks with tunable mechanical and degradation properties through simple changes during Acr-PGS synthesis. For example, the number of acrylate functional groups on the macromer dictates the concentration of crosslinks formed in the resulting network. Three macromers were synthesized that form networks that vary dramatically with respect to their tensile modulus (~30 kPa to 6.6 MPa) and degradation behavior (~20 to 100% mass loss at 12 weeks) based on the extent of acrylation (~1 to 24%). These macromers were processed into biodegradable fibrous scaffolds using electrospinning, with gelatin as a carrier polymer to facilitate fiber formation and cell adhesion. The resulting scaffolds were also diverse with respect to their mechanics (tensile modulus ranging from ~60 kPa to 1 MPa) and degradation (~45 to 70% mass loss by 12 weeks). Mesenchymal stem cell adhesion and proliferation on all fibrous scaffolds was indistinguishable from controls. The scaffolds showed similar diversity when implanted on the surface of hearts in a rat model of acute myocardial infarction and demonstrated a dependence on scaffold thickness and chemistry in the host response. In summary, these diverse scaffolds with tailorable chemical, structural, mechanical and degradation properties are potentially useful for the engineering of a wide range of soft tissues.Biomedical engineeringgv2131, gme2103Medicine, Biomedical EngineeringArticlesMicrogravity Studies of Cells and Tissues: from Mir to ISShttp://academiccommons.columbia.edu/catalog/ac:169000
Vunjak-Novakovic, Gordana; Preda, Carmen; Bordonaro, Julie; Pellis, Neal; de Luis, Javier; Freed, Lisa E.http://dx.doi.org/10.7916/D8CZ3543Thu, 23 Jan 2014 00:00:00 +0000In vitro studies of cells and tissues in microgravity, either simulated by cultivation conditions on earth or reduced by spaceflight, are essential for the identification of mechanisms underlying gravity sensing and transduction in biological organisms. In this paper, we review rotating bioreactor studies of engineered skeletal and cardiovascular tissues carried out in unit gravity, a Shuttle-Mir study of cartilage tissue engineering, and the ongoing development and testing of a Cell Culture Unit for cell and tissue cultivation aboard the ISS.Biomedical engineeringgv2131Biomedical EngineeringArticlesExposing Internal Attentional Brain States using Single-Trial EEG Analysis with Combined Imaging Modalitieshttp://academiccommons.columbia.edu/catalog/ac:182030
Walz, Jenniferhttp://dx.doi.org/10.7916/D8PK0D4VWed, 22 Jan 2014 00:00:00 +0000The goal of this dissertation is to explore the neural correlates of endogenous task-related attentional modulations. Natural fluctuations in task engagement are challenging to study, primarily because they are by nature not event related and thus cannot be controlled experimentally. Here we exploit well-accepted links between attention and various measures of neural activity while subjects perform simple target detection tasks that leave their minds free to wander. We use multimodal neuroimaging, specifically simultaneous electroencephalograpy and functional magnetic resonance imaging (EEG-fMRI) and EEG-pupillometry, with data-driven machine learning methods and study activity across the whole brain. We investigate BOLD fMRI correlates of EEG variability spanning each trial, enabling us to unravel a cascade of attention-related activations and determine their temporal ordering. We study activity during auditory and visual paradigms independently, and we also combine data to investigate supra modal attention systems. Without aiming to study known attention-related functional brain networks, we found correlates of attentional modulations in areas representative of the default mode network (DMN), ventral attention network (VAN), locus coeruleus norepinephrine (LC-NE) system, and regions implicated in generation of the extensively-studied P300 EEG response to target stimuli. Our results reveal complex interactions between known attentional systems, and do so non-invasively to study normal fluctuations of task engagement in the human brain.Biomedical engineering, Neurosciencesjw2552Biomedical EngineeringDissertationsBone Tissue Engineering with Human Stem Cellshttp://academiccommons.columbia.edu/catalog/ac:168825
Vunjak-Novakovic, Gordana; Marolt, Darja; Knezevic, Miomirhttp://dx.doi.org/10.7916/D83R0QT0Tue, 21 Jan 2014 00:00:00 +0000Treatment of extensive bone defects requires autologous bone grafting or implantation of bone substitute materials. An attractive alternative has been to engineer fully viable, biological bone grafts in vitro by culturing osteogenic cells within three-dimensional scaffolds, under conditions supporting bone formation. Such grafts could be used for implantation, but also as physiologically relevant models in basic and translational studies of bone development, disease and drug discovery. A source of human cells that can be derived in large numbers from a small initial harvest and predictably differentiated into bone forming cells is critically important for engineering human bone grafts. We discuss the characteristics and limitations of various types of human embryonic and adult stem cells, and their utility for bone tissue engineering.Biomedical engineeringgv2131, dm2453Biomedical EngineeringArticlesPhysical Influences on Stem Cellshttp://academiccommons.columbia.edu/catalog/ac:168828
Vunjak-Novakovic, Gordanahttp://dx.doi.org/10.7916/D8028PG9Tue, 21 Jan 2014 00:00:00 +0000Treatment of extensive bone defects requires autologous bone grafting or implantation of bone substitute materials. An attractive alternative has been to engineer fully viable, biological bone grafts in vitro by culturing osteogenic cells within three-dimensional scaffolds, under conditions supporting bone formation. Such grafts could be used for implantation, but also as physiologically relevant models in basic and translational studies of bone development, disease and drug discovery. A source of human cells that can be derived in large numbers from a small initial harvest and predictably differentiated into bone forming cells is critically important for engineering human bone grafts. We discuss the characteristics and limitations of various types of human embryonic and adult stem cells, and their utility for bone tissue engineering.Biomedical engineeringgv2131Biomedical EngineeringArticlesPercutaneous Cell Delivery Into the Heart Using Hydrogels Polymerizing In Situhttp://academiccommons.columbia.edu/catalog/ac:168982
Vunjak-Novakovic, Gordana; Martens, Timothy P.; Godier, Amandine F. G.; Parks, Jonathan J.; Wan, Leo Q.; Koeckert, Michael S.; Eng, George M.; Hudson, Barry I.; Sherman, Warrenhttp://dx.doi.org/10.7916/D8V9861VTue, 21 Jan 2014 00:00:00 +0000Heart disease is the leading cause of death in the US. Following an acute myocardial infarction, a fibrous, noncontractile scar develops, and results in congestive heart failure in more than 500,000 patients in the US each year. Muscle regeneration and the induction of new vascular growth to treat ischemic disorders of the heart can have significant therapeutic implications. Early studies in patients with chronic ischemic systolic left ventricular dysfunction (SLVD) using skeletal myoblasts or bone marrow-derived cells report improvement in left ventricular ejection function (LVEF) and clinical status, without notable safety issues. Nonetheless, the efficacy of cell transfer for cardiovascular disease is not established, in part due to a lack of control over cell retention, survival, and function following delivery. We studied the use of biocompatible hydrogels polymerizable in situ as a cell delivery vehicle, to improve cell retention, survival, and function following delivery into the ischemic myocardium. The study was conducted using human bone marrow-derived mesenchymal stem cells and fibrin glue, but the methods are applicable to any human stem cells (adult or embryonic) and a wide range of hydrogels. We first evaluated the utility of several commercially available percutaneous catheters for delivery of viscous cell/hydrogel suspensions. Next we characterized the polymerization kinetics of fibrin glue solutions to define the ranges of concentrations compatible with catheter delivery. We then demonstrate the in vivo effectiveness of this preparation and its ability to increase cell retention and survival in a nude rat model of myocardial infarction.Biomedical engineeringgv2131, afg2109, gme2103, ws2157Medicine, Biomedical EngineeringArticlesBiomechanical Assessment and Monitoring of Thermal Ablation Using Harmonic Motion Imaging for Focused Ultrasound (HMIFU)http://academiccommons.columbia.edu/catalog/ac:168502
Hou, Yihttp://dx.doi.org/10.7916/D8FJ2DR5Mon, 06 Jan 2014 00:00:00 +0000Cancer remains, one of the major public health problems in the United States as well as many other countries worldwide. According to According to the World Health Organization, cancer is currently the leading cause of death worldwide, accounting for 7.6 million deaths annually, and 25% of the annual death was due to Cancer during the year of 2011. In the long history of the cancer treatment field, many treatment options have been established up to date. Traditional procedures include surgical procedures as well as systemic therapies such as biologic therapy, chemotherapy, hormone therapy, and radiation therapy. Nevertheless, side-effects are often associated with such procedures due to the systemic delivery across the entire body. Recently technologies have been focused on localized therapy under minimally or noninvasive procedure with imaging-guidance, such as cryoablation, laser ablation, radio‐frequency (RF) ablation, and High Intensity F-ocused Ultrasound (HIFU). HIFU is a non-invasive procedure aims to coagulate tissue thermally at a localized focal zone created with noninvasively emitting a set of focused ultrasound beams while the surrounding healthy tissues remain relatively untreated. Harmonic Motion Imaging for Focused Ultrasound (HMIFU) is a dynamic, radiation-force-based imaging technique, which utilizes a single HIFU transducer by emitting an Amplitude-modulated (AM) beam to both thermally ablate the tumor while inducing a stable oscillatory tissue displacement at its focal zone. The oscillatory response is then estimated by a cross-correlation based motion tracking technique on the signal collected by a confocally-aligned diagnostic transducer. HMIFU addresses the most critical aspect and one of the major unmet needs of HIFU treatment, which is the ability to perform real-time monitoring and mapping of tissue property change during the HIFU treatment. In this dissertation, both the assessment and monitoring aspects of HMIFU have been investigated fundamentally and experimentally through development of both a 1-D and 2-D based system. The performance assessment of HMIFU technique in depicting the lesion size increase as well as the lesion-to-background displacement contrast was first demonstrated using a 3D, FE-based interdisciplinary simulation framework. Through the development of 1-D HMIFU system, a multi-parametric monitoring approach was presented where presented where the focal HMI displacement, phase shift (Δφ), and correlation coefficients were monitored along with thermocouple and PCD under the HIFU treatment sequence with boiling and slow denaturation. For HIFU treatments with slow denaturation, consistent displacement increase-then-decrease trend was observed, indicating tissue softening-then-stiffening and phase shift increased with treatment time in agreement with mechanical testing outcomes. The correlation coefficient remained high throughout the entire treatment time under a minimized broadband energy and boiling mechanism. Contrarily, both displacement and phase shift changes lacked consistency under HIFU treatment sequences with boiling due to the presence of strong boiling mechanism confirmed by both PCD and thermocouple monitoring. In order to facilitate its clinical translation, a fully-integrated, clinically 2D real-time HMIFU system was also developed, which is capable of providing 2D real-time streaming during HIFU treatment up to 15 Hz without interruption. Reproducibility studies of the system showed consistent displacement estimation on tissue-mimicking phantoms as well as monitoring of tissue-softening-then-stiffening phase change across 16 out of 19 liver specimens (Increasing rate in phase shift (Δφ): 0.73±0.69 %/s, Decreasing rate in phase shift (Δφ): 0.60±0.19 %/s) along with thermocouple monitoring (Increasing: 0.84±1.15 %/ °C, Decreasing: 2.03± 0.93%/ °C) and validation of tissue stiffening using mechanical testing. In addition, the 2-D HMIFU system feasibility on preclinical pancreatic tumor mice model was also demonstrated in vivo, where HMI displacement decreases were observed across three of five treatment locations on the kP(f)c model at 20.8±6.84, 18.6±1.46, and 24.0±5.43%, as well as across four of the seven treatment locations on the KPC model at 39.5±2.98%, 34.5±21.5%, 16.0±3.05%, and 35.0±3.12% along with H and E histological confirmation. In order to improve the quantitative monitoring aspect of HMIFU, a novel, model-independent method for the estimating Young's modulus based on strain profile was also implemented, where 1-D HMIFU system showed feasibilities on polyacrylamide phantom (EHMI/E ≈ 2.3) and liver specimen (EHMI/E ≈ 8.1), and 2-D HMIFU system showed feasibilities on copolymer phantom(EHMI/E ≈ 30.4), liver specimen(EHMI/E ≈ 211.3), as well as HIFU treated liver specimen(EHMI,end/EHMI,beginning ≈ 5.96). In conclusion, the outcomes from the aforementioned studies successfully showed the feasibility of both HMIFU systems in multi-parametric monitoring of HIFU treatment with slow denaturation and boiling, which prepares its stage towards clinical translation.Biomedical engineering, Biomechanics, Acousticsyh2367Biomedical EngineeringDissertationsIdentification of Key Structural Elements of ATP-Dependent Molecular Motorshttp://academiccommons.columbia.edu/catalog/ac:168511
Zhang, Yuanhttp://dx.doi.org/10.7916/D82805JNMon, 06 Jan 2014 00:00:00 +0000Molecular motors perform diverse functions in cells, ranging from muscle contraction, cell division, DNA/RNA replication, protein degradation, and vesicle transport. The majority of molecular motors use energy from the ATP hydrolysis cycle, converting chemical energy into mechanical work in cells. All ATP-dependent molecular motors have a similar ATP binding site, although the functions can be drastically different. Myosins comprise a large group of ATP-dependent molecule motors. The structure-function relationship governing different functions for different myosin families remains elusive. Hypothesizing that members of each family possess conserved residues for their consensus functions and residues distinctive from those of other families to differentiate their functions from functions of other myosin families, we developed an algorithm for comparative sequence analysis in a phylogenic hierarchy to identify family-specific residues for 38 myosin families/subfamilies that comprise human myosin members. We found a number of family-specific residues that have been reported, such as residues in β-cardiac myosin associated with hypertrophic cardiomyopathy and residues in myosin 7A associated with hereditary deafness. We also identified distinct features among myosin families that have never been reported, including a unique signature of the SH1 domain in each of the myosin families, residues differentiating α- and β-cardiac myosins, and a unique converter domain of myosin VI. We further examined myosin VI to understand why it moves toward the (-)-end of actin filaments, opposite to the direction of all other myosins and to shed light on their links to prostate cancer and ovarian cancer, where myosin VI is over-expressed. We found that many of myosin VI specific residues locate in or adjacent to the converter domain, including a cluster of unique residues at the interface between the motor domain and the converter. Using molecular dynamics (MD) simulation, we found mutations of M701 on the SH1 helix and F763 on a helix of the converter caused the separation of the motor domain and the converter, indicating their important roles in linking the converter and the motor domain in the pre-power stroke state structure, potentially critical for positioning of lever arm. Using the location of the unique residues at the interface of the motor domain and the converter as the site of drug docking, we identified a set of candidate small molecules binding to this unique binding site selectively, potentially blocking the converter rotation of myosin VI. A benzoic acid (C15H17N3O3) was found to have the best score in docking, binding to both the converter and motor domain stably in a 200 ns MD simulation run. This molecule can be a good lead to be optimized to inhibit myosin VI functions in cancer patients. We have also applied our algorithm to other ATP-dependent molecular motors, including hepatitis C virus NS3 helicase and DEAD box helicase Mss116. We found an important residue, T324, in NS3 helicase connecting domains 1 and 2 acting as a flexible hinge for opening of the ATP-binding cleft and an atomic interaction cascade from T324 to residues in domains 1 and 2 controls the flexibility of the ATP-binding cleft in NS3 helicase. We also found a conserved flexible linker for Mss116, and the tight interactions between the Mss116-specific flexible linker and the two RecA-like domains are mechanically required to crimp RNA for the unique RNA processes of yeast Mss116.Biomedical engineeringyz2307Mechanical EngineeringDissertationsQuantifying Structural and Functional Changes in Cardiac Cells in an In Vitro Model of Diabetic Cardiomyopathyhttp://academiccommons.columbia.edu/catalog/ac:168472
Michaelson, Jarett Evanhttp://dx.doi.org/10.7916/D88050K1Mon, 06 Jan 2014 00:00:00 +0000Diabetes Mellitus is one of the most common diseases in the world. Cardiovascular diseases account for ~80% of deaths amongst diabetic patients, primarily through coronary artery disease (CAD). However, a new clinical entry, termed Diabetic Cardiomyopathy (DC), may lead to heart failure in diabetic patients independently of CAD or hypertension. In DC, hyperglycemia and hyperlipidemia associated with diabetes produce structural and biochemical alterations at the cardiac cell level. Early stage cell alterations include hypertrophy, calcium mishandling, cell apoptosis, excessive ROS production, and increased collagen production by fibroblasts. Eventually, major structural and functional changes can appear in myocardial tissue, characterized by diastolic and systolic dysfunction, and eventually heart failure. While specific changes associated with DC are well characterized, the mechanism underlying disease development and progression as a whole remain to be elucidated. The ability of researchers to develop general treatment options for this disease is thus limited. Currently, a majority of DC studies focus on either in vitro molecular pathways, or in vivo whole-heart properties such as ejection fraction. However, as DC is primarily a disease of changes in structural and functional properties, these studies can not precisely quantify what conditions (such as hyperglycemia and hyperlipidemia) are producing specific biomechanical changes such as increased myocardial stiffness or diastolic dysfunction. To address this, we developed an in vitro approach, based on culturing cardiac cells in elevated glucose and fatty acid, to examine how structural and functional properties may change as a result of a diabetic environment. Increased myocardial stiffness is associated with increased collagen production in the heart. However, diastolic dysfunction is found to occur in DC prior to significant collagen accumulation. We hypothesized that increased cardiac cell stiffness could contribute to early stage diastolic dysfunction. To test this hypothesis, we developed and used contemporary biomedical engineering tools to characterize the biomechanical properties of cardiac myocytes and fibroblasts under a variety of hyperglycemic and hyperlipidemic conditions. We showed that our in vitro model of DC exhibits increased stiffness in myocytes, but not fibroblasts. We then developed an assay to measure cardiac myocyte contractile force, as well as assess systolic and diastolic function. This assay was then used to determine the role of N-acetyl-cysteine (NAC), towards regulating reactive oxygen species (ROS) and reversing cellular-level changes associated with our DC model. We found that DC model cardiac myocytes exhibited greater incidences of diastolic, but not systolic, dysfunction, and that treatment with NAC reduced dysfunction to a normal level. In terms of structural properties, we additionally determined that treatment with NAC attenuated increases in myocyte stiffness found in our DC model, and that NAC reduced myocyte hypertrophy for certain diabetic conditions. Overall, treatment with NAC attenuates the maladaptive mechanical and functional changes found in our DC model.Biomedical engineeringjem2199Biomedical EngineeringDissertationsDevelopment and applications of high speed and hyperspectral nonlinear microscopyhttp://academiccommons.columbia.edu/catalog/ac:178480
Grosberg, Laurenhttp://hdl.handle.net/10022/AC:P:22144Thu, 07 Nov 2013 00:00:00 +0000Nonlinear microscopy refers to a range of laser scanning microscopy techniques that are based on nonlinear optical processes such as two-photon excited fluorescence and second harmonic generation. Nonlinear microscopy techniques are powerful because they enable the visualization of highly scattering biological samples with subcellular resolution. This capability is especially valuable for in vivo and live tissue imaging since it can provide both structural and functional information about tissues in their native environment. With the use of a range of exogenous dyes and intrinsic contrast, in vivo nonlinear microscopy can be used to characterize and measure dynamic processes of tissues in their normal environment. These advances have been particularly relevant in neuroscience, where truly understanding the function of the brain requires that its neural and vascular networks be observed while undisturbed. Despite these advantages, in vivo nonlinear microscopy still faces several major challenges. First, observing dynamics that occur in large areas over short time scales, such as neuronal signaling and blood flow, is challenging because nonlinear microscopy generally requires scanning to create an image. This limits the study of dynamic behavior to either a single plane or to a small subset of regions within a volume. Second, applications that rely on the use of exogenous dyes can be limited by the need to stain tissues before imaging, the availability of dyes, and specificity that can be achieved. Usually considered a nuisance, endogenous tissue contrast from autofluorescence or structures exhibiting second harmonic generation can produce stunning images for visualizing subcellular morphology. Imaging endogenous contrast can also provide valuable information about the chemical makeup and metabolic state of the tissue. Few methods have been developed to carefully and quantitatively examine endogenous fluorescence in living tissues. In this thesis, these two challenges in nonlinear microscopy are addressed. The development of a novel hyperspectral two-photon microscopy method to acquire spectroscopic data from tissues and increase the information available from endogenous contrast is presented. This system was applied to visualize and identify sources of endogenous contrast in gastrointestinal tissues, providing robust references for the assessment of normal and diseased tissues. Secondly, three methods for high speed volumetric imaging using laser scanning nonlinear microscopy were developed to address the need for improved high-speed imaging in living tissues. A spectrally-encoded high-speed imaging method that can provide simultaneous imaging of multiple regions of the living brain in parallel is presented and used to study spontaneous changes in vascular tone in the brain. This technique is then extended for use with second harmonic generation microscopy, which has the potential to greatly increase the degree of multiplexing. Finally, a complete system design capable of volumetric scan rates >1Hz is shown, offering improved performance and versatility to image brain activity.Biomedical engineeringBiomedical EngineeringDissertationsPreconditioning Methods in Cartilage Tissue Engineering: Influences of Silk Material Properties and Hypoxia on Chondrogenesishttp://academiccommons.columbia.edu/catalog/ac:177276
Yodmuang, Supansahttp://hdl.handle.net/10022/AC:P:22003Thu, 17 Oct 2013 00:00:00 +0000Cartilage has limited intrinsic healing potential, due to the low cell density and the lack of blood supply. Current treatments for cartilage repair rarely restore full structure and function to the native state. Tissue engineering holds promise to create cartilage grafts capable to withstand the stresses present in joints. More than 90% of articular cartilage tissue is composed of extracellular matrix and is located in the loading environment under low oxygen tension in knee joints. To form engineered constructs with mechanical properties compatible to native tissue, scaffolds should provide structural support, maintain cell phenotype and subsequently promote tissue development. The focus of this dissertation is on utilizing the physiological conditions found in joints to regulate biological behavior of cells. The first factor that was studied was the extracellular matrix. Two formats of silk fibroin-hydrogel and porous scaffolds - were examined for their potential as a supporting material for creating cartilage tissue constructs. The composite silk made from nano-fibers and hydrogel - a structure resembling the collagen network and proteoglycan in native cartilage - improved equilibrium and dynamic modulus of engineered tissue by 50% and 60%, respectively, in comparison to silk hydrogel without fibers. The second factor studied was the modulation of oxygen level, which is a major regulator during native cartilage development. Chondrogenic differentiation was induced in human embryonic stem cells under hypoxic conditions, in conjunction with biochemical cues from bovine chondrocytes. As a result, SOX9, a key transcription factor of cartilaginous lineage, was upregulated in the induced cells. Subsequent cultivation under normoxic conditions resulted in robust formation of cartilage tissue. Taken together, studies conducted in my thesis work address two major challenges in cartilage tissue engineering: i) providing cells with structural and mechanical properties similar to native ECM for generating in vitro cartilaginous tissue and ii) preconditioning cells with physiological environment for directing chondrogenic differentiation.Biomedical engineering, BiologyBiomedical EngineeringDissertationsIn-Vivo Three Dimensional Proton Hadamard Spectroscopic Imaging in the Human Brainhttp://academiccommons.columbia.edu/catalog/ac:165932
Cohen, Ourihttp://hdl.handle.net/10022/AC:P:21844Fri, 27 Sep 2013 00:00:00 +0000Magnetic resonance spectroscopic imaging (MRSI) is a useful tool for obtaining information on the biochemical processes underlying various pathologies. A widely used multi-voxel localization method is chemical shift imaging (CSI) which uses gradients for phase encoding. Although simple to implement, low in specific absorption rate (SAR) and immune to chemical shift displacement (CSD), it also suffers from some well known drawbacks caused by its sinc-shaped point spread function (PSF). This results in loss of both signal-to-noise ratio (SNR) as well as localization, an effect that is exacerbated at low resolutions. In contrast, an alternative localization method, Hadamard spectroscopic imaging (HSI) benefits from a theoretically ideal PSF and consequently does not suffer from these drawbacks. In this work we exploit the theoretically ideal PSF of HSI encoding to develop a novel three dimensional (3D) multi-voxel MR localization method based on transverse HSI (T-HSI). The advantages of T HSI are that unlike gradient phase-encoding: (i) the volume of interest (VOI) does not need to be smaller than the field-of-view to prevent aliasing; (ii) the number of partitions in each direction can be small, 8, 4 or even 2 at no cost in PSF; (iii) the VOI does not have to be contiguous; and (iv) the voxel profile depends on the available B1 and pulse synthesis paradigm and can therefore, at least theoretically, approach "ideal" "1" inside and "0" elsewhere. Clinical utility of the new method is shown by spectra obtained from the brain of a healthy volunteer. The benefits of T-HSI are demonstrated by a quantitative comparison to CSI of the SNR and localization in a phantom in both one and three dimensions at clinical resolutions. A novel matrix formalism is used to quantify the impact of non-ideal flip angles on T-HSI. The superior PSF of T-HSI is then used to demonstrate the feasibility of scanning regions near or on the skull while limiting the impact of lipid contamination and obtaining quantifiable spectra. A comparison to spectra obtained using CSI is shown for a healthy volunteer. The new method is also used in a clinical pathology: to scan multiple sclerosis (MS) lesions occurring near the skull. To maintain the benefits provided by the PSF of HSI at higher fields, despite its susceptibility to CSD, a additional hybrid sequence is also developed that limits both the SAR and the CSD, regardless of the size of the VOI. A comparison to CSI in a phantom and in-vivo is carried out and spectra obtained from the brain of a healthy volunteer at 3T are shown. Finally, future research avenues involving extension of this research to ultra high fields (7T) are discussed and possible clinical uses are described.Biomedical engineering, Medical imaging and radiologyBiomedical EngineeringDissertationsNon-contrast Magnetic Resonance Angiography for Evaluation of Peripheral Arterial Diseasehttp://academiccommons.columbia.edu/catalog/ac:164224
Atanasova, Iliyanahttp://hdl.handle.net/10022/AC:P:21324Wed, 14 Aug 2013 00:00:00 +0000Peripheral arterial disease (PAD) is a major cause of morbidity and mortality in the USA with an estimated prevalence of up to 20% in those over 75 years. Vascular disease and kidney impairment frequently coexist; prevalence of moderate to severe renal dysfunction in PAD patients is estimated at 27-36%. Knowledge of location, severity, and extent of PAD is imperative for accurate diagnosis and treatment planning. However, all established imaging modalities that are routinely used for treatment planning are contra-indicated in kidney disease patients. Contrast-enhanced x-ray and CT angiography are unsafe due to exposure to nephrotoxic contrast material and ionizing radiation. Recently, the FDA has also warned against the use of gadolinium-enhanced MRA (Gd-MRA) due to evidence that gadolinium could trigger a life-threatening condition known as nephrogenic systemic fibrosis (NSF) in patients with moderate to severe kidney dysfunction. There is a clinical need to develop vascular imaging techniques that are safe in patients with coexisting PAD and renal insufficiency. The focus of this thesis was the development of a non-contrast alternative to Gd-MRA for imaging of peripheral vessels from renal to pedal arteries with MRI. A new imaging sequence for non-contrast visualization of the abdominal and pelvic arteries was designed, implemented, and validated in a small cohort of PAD patients against Gd-MRA. In addition, an existing fast spin-echo based technique for unenhanced imaging of the lower extremities was optimized for improved performance in a clinical setting.Medical imaging and radiology, Biomedical engineeringBiomedical EngineeringDissertationsFirst in vivo Real-Time Imaging of Endocardial RF Ablation by Optical Coherence Tomographyhttp://academiccommons.columbia.edu/catalog/ac:164061
Fleming, Christine P.; Rosenthal, Noah; Rollins, Andrew M.; Arruda, Mauriciohttp://hdl.handle.net/10022/AC:P:21305Wed, 07 Aug 2013 00:00:00 +0000We report the first in vivo use of optical coherence tomography (OCT), a high-resolution (~10 µm) real-time imaging technology, to scan subendocardial tissue and to monitor radiofrequency (RF) lesion formation. Endocardial imaging during an open chest procedure in a female pig was conducted with a forward imaging catheter with a Fourier Domain OCT system at 20 frames per second. Images of the endocardial surface and subendocardial tissue were obtained when the catheter was in direct contact with the endocardial surface. The formation and progressive increase in size of cavities within the myocardium were observed in the OCT images when a steam pop was audible. Our initial findings suggest that imaging with a forward scanning OCT catheter can assess tip electrode–tissue interface contact, image subsurface myocardial structure, and visualize dynamic effects of intramural RF energy delivery.Biomedical engineering, Medical imaging and radiologycpf2115Electrical EngineeringArticlesDepth resolved detection of lipid using spectroscopic optical coherence tomographyhttp://academiccommons.columbia.edu/catalog/ac:163605
Fleming, Christine P.; Eckert, Jocelyn; Halpern, Elkan F.; Gardecki, Joseph A.; Tearney, Guillermo J.http://hdl.handle.net/10022/AC:P:21174Thu, 25 Jul 2013 00:00:00 +0000Optical frequency domain imaging (OFDI) can identify key components related to plaque vulnerability but can suffer from artifacts that could prevent accurate identification of lipid rich regions. In this paper, we present a model of depth resolved spectral analysis of OFDI data for improved detection of lipid. A quadratic Discriminant analysis model was developed based on phantom compositions known chemical mixtures and applied to a tissue phantom of a lipid-rich plaque. We demonstrate that a combined spectral and attenuation model can be used to predict the presence of lipid in OFDI images.Biomedical engineering, Opticscpf2115Electrical EngineeringArticlesPrePPI: a structure-informed database of protein–protein interactionshttp://academiccommons.columbia.edu/catalog/ac:163131
Zhang, Qiangfeng Cliff; Petrey, Donald S.; Garzon Canas, Jose I.; Deng, Lei; Honig, Barryhttp://hdl.handle.net/10022/AC:P:21030Thu, 11 Jul 2013 00:00:00 +0000PrePPI (http://bhapp.c2b2.columbia.edu/PrePPI) is a database that combines predicted and experimentally determined protein–protein interactions (PPIs) using a Bayesian framework. Predicted interactions are assigned probabilities of being correct, which are derived from calculated likelihood ratios (LRs) by combining structural, functional, evolutionary and expression information, with the most important contribution coming from structure. Experimentally determined interactions are compiled from a set of public databases that manually collect PPIs from the literature and are also assigned LRs. A final probability is then assigned to every interaction by combining the LRs for both predicted and experimentally determined interactions. The current version of PrePPI contains ∼2 million PPIs that have a probability more than ∼0.1 of which ∼60 000 PPIs for yeast and ∼370 000 PPIs for human are considered high confidence (probability greater than 0.5). The PrePPI database constitutes an integrated resource that enables users to examine aggregate information on PPIs, including both known and potentially novel interactions, and that provides structural models for many of the PPIs.Biochemistry, Molecular biology, Biomedical engineeringqz2126, dsp18, jig2114, ld2540, bh6Biochemistry and Molecular Biophysics, Civil Engineering and Engineering Mechanics, Howard Hughes Medical InstituteArticlesEffects of Interfacial Geometry on Laser Joining of Dissimilar NiTi to Stainless Steel Wireshttp://academiccommons.columbia.edu/catalog/ac:162947
Brandal, Grant Bjørn; Satoh, Gen; Yao, Y. Lawrence; Naveed, Syedhttp://hdl.handle.net/10022/AC:P:20966Tue, 09 Jul 2013 00:00:00 +0000Joining of the dissimilar metal pair NiTi to stainless steel is of great interest for implantable biomedical applications. Formation of brittle intermetallic phases requires that the joining processes limit the amount of over-melting and mixing along the interface. Thus, laser joining is a preferred method due to its ability to precisely control heat input. This study explores a method of using a cup and cone interfacial geometry, with no filler material, to increase the tensile strength of the joint. Not only does the cup and cone geometry increase the surface area of the interface, but it also introduces a shear component, which is shown to be beneficial to tensile strength of the wire as well. The fracture strength for various cone apex angles and laser powers is determined. Compositional profiles of the interfaces are analyzed. A numerical model is used for explanation of the processing.Biomedical engineering, Materials sciencegbb2114, yly1Mechanical EngineeringPresentationsLaser Autogenous Brazing of Biocompatible, Dissimilar Metals in Tubular Geometrieshttp://academiccommons.columbia.edu/catalog/ac:162950
Satoh, Gen; Brandal, Grant Bjørn; Yao, Y. Lawrence; Naveed, Syedhttp://hdl.handle.net/10022/AC:P:20967Tue, 09 Jul 2013 00:00:00 +0000The successful joining of dissimilar metal tubes would enable the selective use of the unique properties exhibited by biocompatible materials such as stainless steel and shape memory materials such as NiTi, to locally tailor the properties of implantable medical devices. The lack of robust joining processes for the dissimilar metal pairs found within these devices, however, is an obstacle to their development and manufacture. Traditional joining methods suffer from weak joints due to the formation of brittle intermetallics or use filler materials that are unsuitable for use within the human body. This study investigates a new process, Laser Autogenous Brazing, that utilizes a thermal accumulation mechanism to form joints between dissimilar metals without filler materials. This process has been shown to produce robust joints between wire specimens but requires additional considerations when applied to tubular parts. The strength, composition, and microstructure of the resultant joints between NiTi and Stainless Steel are investigated and the effects of laser parameters on the thermal profile and joining mechanism are studied through experiments and numerical simulations.Biomedical engineering, Materials sciencegbb2114, yly1Mechanical EngineeringPresentationsDynamic Digital Optical Tomography for Cancer Imaging and Therapy Monitoringhttp://academiccommons.columbia.edu/catalog/ac:159181
Flexman, Mollyhttp://hdl.handle.net/10022/AC:P:19424Mon, 25 Mar 2013 00:00:00 +0000Diffuse optical tomography is a non-invasive imaging technique that uses near-infrared light to create three-dimensional images of tissue. This dissertation presents the design and validation of an instrument for rapid optical imaging using digital detection techniques. In addition to a detailed description of the instrument, three studies are presented: a clinical study detecting breast cancer using dynamic optical imaging; a pre-clinical study monitoring early tumor response to anti-angiogenic therapy; and a clinical study monitoring individual patient response to neoadjuvant chemotherapy. These studies show that diffuse optical tomography is a valuable imaging modality that can play an important role in cancer detection and treatment.Biomedical engineering, Engineeringmlf2129Biomedical EngineeringDissertationsQuantifying Atherosclerosis: IVUS Imaging For Lumen Border Detection And Plaque Characterizationhttp://academiccommons.columbia.edu/catalog/ac:159166
Katouzian, Aminhttp://hdl.handle.net/10022/AC:P:19158Mon, 25 Feb 2013 00:00:00 +0000The importance of atherosclerotic disease in coronary artery has been a subject of study for many researchers in the past decade. In brief, the aim is to understand progression of such a disease, detect plaques at risks (vulnerable plaques), and treat them selectively to prevent mortality and immobility. Consequently, several imaging modalities have been developed and among them intravascular ultrasound (IVUS) has been of particular interest since it provides useful information about tissues microstructures and images with sufficient penetration as well as resolution. In general, the ultimate goal is to provide interventional cardiologists with reliable clinical tools so they can identify vulnerable plaques, make decisions confidently, choose the most appropriate drugs or implant devices (i.e. stent), and stabilize them during catheterization procedures with minimal risk. In this work, we review existing atherosclerotic tissue characterization algorithms including the state-of-the-art virtual histology (VH) framework, which has been implemented in the Volcano (Rancho Cordova, CA) IVUS clinical scanners using 64-elements 20 MHz phased-array transducer. Initially, we intended to extend this technique for data acquired with 40 MHz single-element transducers. For this reason, we started acquiring in vitro IVUS data and studied involved challenges from specimen preparation toward classification. We observed inconsistency among extracted features along with transducer's spectral parameters (i.e. bandwidth, center frequency). This, in addition to infeasibility of construction of reliable training dataset due to heterogeneity of atherosclerotic tissues motivated us to develop an unsupervised texture-based atherosclerotic tissue characterization algorithm. We proposed a two-dimensional multiscale wavelet-based algorithm to expand IVUS backscattered signals and/or grayscale images onto orthogonal symmetric quadrature mirror filters (QMF) such as Lemarie-Battle. At the bottom of decomposition tree, we employed ISODATA to cluster enveloped detected features in an unsupervised fashion and classify atherosclerotic plaque constitutes into fibrotic, lipidic, calcified, and no tissues. For the first time, we studied numbers of factors that were necessary for extension of in vitro derived classifier for in vivo applications such as reliability of classified tissues behind arc of calcified plaques and effects of pressure changes as well as flowing blood on constructed tissue color maps, called prognosis histology (PH) images. The second half of this dissertation is devoted to automatic detection of lumen borders in IVUS grayscale images acquired with high frequency (40 MHz up) transducers where more scattering exhibited within lumen area that makes the problem of interest more challenging. We established our framework on three-dimensional expansion of IVUS sub-volumes onto orthonormal brushlet basis function. The rational behind our framework was presence of incoherent (i.e. blood) versus coherent (i.e. plaque, surrounding fat) textural patterns along pullback direction, which was motivated by what an interventional cardiologist does to locate the lumen border visually by going back and forth among IVUS frames. We studied the feasibility of brushlet analysis through filtering blood speckles and supervised classification of blood versus non-blood regions. Our preliminary study confirmed that the most informative features reside in the innermost cubes, representing low-frequency components in transformed domain. Finally, we explored that tissue responses to IVUS signals are proportionally preserved in brushlet coefficients and it enabled us to classify blood regions in complex brushlet space. Subsequently, we employed surface function actives (SFA) to estimate the lumen borders after regularization. In a comparison study, we quantified our results with two of existing algorithms, employing IVUS grayscale images acquired with 40 MHz and 45 MHz single-element transducers. Overall, our proposed algorithm outperformed and the resulting automated detected borders showed good correlation with manually traced borders by an expert.Biomedical engineeringBiomedical EngineeringDissertationsNoise Optimization for High-Bandwidth Ion Channel Recordingshttp://academiccommons.columbia.edu/catalog/ac:183392
Rosenstein, Jacobhttp://hdl.handle.net/10022/AC:P:19133Wed, 20 Feb 2013 00:00:00 +0000Single-molecule measurements often exhibit weak signals and fast kinetics, making them particularly challenging to record with high fidelity. This thesis presents an analysis of voltage-clamp current recordings of single ion channels, and concludes that considerable improvements in signal-to-noise ratios can be achieved by minimizing all parasitic capacitances associated with these measurements. A custom integrated amplifier in a 0.13-micron complementary metal oxide semiconductor (CMOS) process is designed for high-bandwidth ion channel recordings, and systems are designed to closely incorporate this amplifier with solid-state nanopore sensors, lipid membranes, and biological ion channels. The low capacitance of these integrated platforms reduces noise at high frequencies, enabling signals to be measured up to ten times faster than had been previously achieved. In addition to improving signal quality, the small physical size of these integrated systems portends the arrival of massively parallel high-performance ion channel recording systems for drug discovery and biomolecular sensing applications.Electrical engineering, Biophysics, Biomedical engineeringElectrical EngineeringDissertationsMicrofluidic Concentration Gradient Generation and Integrated Magnetic Sorting of Microparticleshttp://academiccommons.columbia.edu/catalog/ac:156763
Zhou, Yaohttp://hdl.handle.net/10022/AC:P:19085Fri, 15 Feb 2013 00:00:00 +0000Microfluidic systems, with their feature size similar to that of biological cells, have great potential for cell manipulation and interrogation. On the other hand, the process of drug discovery involves vast amount of tests of candidate drug molecules with cells, and hence requires intensive manipulation and interrogation of cells. Therefore, it is conceivable that microfluidics can be and should be sufficiently exploited to facilitate drug discovery process. This dissertation investigates two of the most frequently performed cell operations in drug discovery, which are often performed in series, i.e., chemical stimulation of cells (cell treatment and chemotaxis) and cell sorting. For chemical stimulation of cells, rapid and novel designs of concentration gradient generation (CGG) devices are presented; for cell sorting, a magnetically The most prevalent type of CGG devices, i.e., complete mixing-based laminar-flow CGG devices, involves massive channel networks. The design of alternative laminar-flow CGG devices suffers lack of efficient and systematic design framework, and is currently implemented through time-consuming numerical simulations. Therefore, we first propose passive mixing-based laminar-flow CGG devices, for which an analytical diffusion-convection model is developed and incorporated into an iterative design framework to achieve modular design. Secondly, to eliminate the undesirable stimulation of fluid flow on cells as existing in both complete and partial mixing-based laminar-flow CGG devices, a novel class of CGG devices featuring two-layer design sandwiching a semipermeable membrane is presented. The devices effectively eliminate fluid flow while maintain a stable concentration gradient in the gradient generation region. Thirdly, the flow-free CGG devices are extended to realize arbitrary concentration gradients, which significantly enhance the CGG capability of the devices. The designs of all CGG devices are realized through microfabrication and tested against complex concentration gradients. The generated gradients generally agree with the specified gradients in less than 10%. Magnetic-activated cell sorting (MACS) is a high-throughput cell sorting scheme that recognizes cells specifically by their membrane proteins. The quality of magnetic incubation largely determines the final separation efficiency. To enhance magnetic incubation prior to separation, a magnetic incubator is designed utilizing a target acquisition by repetitive traversal (TART) mechanism, which significantly improves target capture efficiency and reduces incubation time. The magnetic incubator module is then integrated to the separator module, with both modules using the same magnetic setup, which facilitates the entire MACS process and promotes the target separation efficiency to over 90%. The microfluidic methods and tools developed in this work are potentially used for cell manipulation and interrogation and thus can be expected to facilitate the drug discovery process that involves intensive cell operations and testing.Biomedical engineering, Mechanical engineeringMechanical EngineeringDissertationsMicrotechnologies for Cardiovascular Tissue Engineeringhttp://academiccommons.columbia.edu/catalog/ac:183407
Eng, Georgehttp://hdl.handle.net/10022/AC:P:19043Wed, 13 Feb 2013 00:00:00 +0000Cardiovascular disease is a rising epidemic worldwide, and curative therapies remain elusive. Heart and vascular disease remain some of the hardest to cure due to the limited capacity of the heart to repair itself, necessitating a cell or organ based therapy to cure the inevitable descent into heart failure. Tissue engineering is uniquely poised to significantly alter this disease burden though the fabrication of cardiac and vascular tissues in vitro. However, the challenges for achieving these aims are significant - for cardiac tissues, the therapy must adhere to strict requirements of adequate perfusion and functional integration with the damaged heart. Vascular tissues are required to be amenable to surgical anastomosis while at the same time provide nutrient transport on the cellular level. Recently, a new set of technologies based from the semiconductor industry, have enabled micron level control over the cellular environment and cells themselves and may enable novel approaches to fulfill these tissue engineering requirements. In this dissertation, these microtechnologies will be leveraged to address some of the current obstacles that limit the use of tissue engineering approaches for functional therapy. Specifically, microtechnologies were used to screen the effect of electrical stimulation on the function and maturation of human embryonic stem cell derived cardiomyocytes, which resulted in the ability to program specific individual beating frequencies of the cells while improving contractile function and led to the identification of a channel specific effect for frequency modulation. These technologies were also used to distinguish the vasculogenic potential of different mesenchymal stem cell sources for nascent vessel stabilization, and enabled the development of a powerful hydrogel docking platform with the novel capability to spatially pattern any number of cells, cytokines or drugs on the microscale, while permitting scale up for larger tissue generation without the loss of precision. Finally, these technologies were used to create vascular networks with hierarchical branching patterns that could be implanted and used in vivo fulfilling a major criterion of vascular tissue function - surgical compatibility with microscale architecture for tissue perfusion. Therefore, these microtechnologies support novel interrogation of cell function and enable new methods to engineer cardiovascular tissues.Biomedical engineeringgme2103Biomedical EngineeringDissertationsApplication of a Novel Quasi-3D Microscopy Technique to Investigate Early Osteocyte Mechanotransduction Eventshttp://academiccommons.columbia.edu/catalog/ac:155913
Baik, Andrewhttp://hdl.handle.net/10022/AC:P:18830Fri, 25 Jan 2013 00:00:00 +0000The objective of this thesis is to observe and characterize the early mechanical and biochemical events in osteocyte mechanotransduction. Physical forces have been increasingly implicated in normal physiological and pathological cellular activities of osteocytes. The mechanotransduction process in osteocytes involves spatiotemporally complex changes in cytoskeletal organization, signal activation, and whole cell mechanical properties. Most in vitro biophysical techniques currently available sacrifice either spatial or temporal resolution and are unable to visualize 3D cellular behavior on the millisecond time scale. Here, we develop a novel multi-channel quasi-3D microscopy technique to simultaneously visualize and measure whole-cell mechanics, intracellular cytoskeletal deformation, and biochemical signal activation under fluid shear flow. The technique was applied to visualize cell dilatation and cytoskeletal deformation in osteocytes under steady fluid shear flow. Analysis of the plasma membrane and either the intracellular actin or microtubule cytoskeletal networks provided characterization of their deformations over time. No volumetric dilatation of the whole cell was observed under flow, and both cytoskeletal networks experienced primarily tensile viscoelastic creep and recovery in all measured strain components. Intra- and inter- cellular mechanical heterogeneity was observed in both cytoskeletal networks. Cytoskeletal disruption pointed towards a unidirectional mechanical interaction where microtubule networks affected actin network strains, but not vice versa. The second study in this thesis investigated the effects of steady and oscillatory flow on the actin and microtubule networks within the same cell. Shear strain was the predominant strain in both steady and oscillatory flows, in the form of viscoelastic creep and elastic oscillations, respectively. Under oscillatory fluid shear flow, the actin networks displayed an oscillatory strain profile more often than the MT networks in all the strains tested and had a higher peak-to-trough magnitude. Taken together with the first study, the actin networks were determined to be the more responsive cytoskeletal networks in osteocytes to fluid flow and may play a bigger role in mechanotransduction. The final culminating study tracked [Ca+2]i and F-actin network strains simultaneously in a single osteocyte. We demonstrated novel osteocyte mechano- and transduction behavior where [Ca+2]i oscillations activate phasic actomyosin contractions using a smooth muscle-like mechanism. Fluid shear, ATP, and ionomycin induced [Ca+2]i signaling with a subsequent compression and recovery in actin strains of the cell, being most apparent in the height direction strain. This contraction was reversible over the period of hundreds of seconds. ML-7, a myosin light chain kinase inhibitor, significantly slowed down the kinetics of contraction initiation, but blebbistatin, a potent skeletal and non-muscle inhibitor, had no effect on the actin contraction. Furthermore, smooth muscle contraction-related proteins were detected by Western blot. The observation of muscle-like contractility in osteocytes demonstrates a possible positive feedback mechanism of osteocytes to activate mechanotransduction pathways.Biomedical engineering, Biomechanicsadb2133Biomedical EngineeringDissertations